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  • International Union of Crystallography (IUCr)  (45,892)
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  • 1
    Publication Date: 2018-12-05
    Description: During screening of the phase space using KOH and 1-methyl-4-aza-1-azoniabicyclo[2.2.2]octane hydroxide (1-methyl-DABCO) under hydrothermal zeolite synthesis conditions, K-paracelsian was synthesized. Scanning electron microscopy, energy dispersive X-ray spectroscopy and ex situ powder X-ray diffraction analysis revealed a material that is compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage. In the case of K-paracelsian it might be useful to consider it a link between feldspars and zeolites. It was also shown that K-paracelsian can be described as the simplest endmember of a family of dense double-crankshaft zeolite topologies. By applying the identified building principle, a number of known zeolite topologies can be constructed. Furthermore, it facilitates the construction of a range of hypothetical small-pore structures that are crystallo-chemically healthy, but which have not yet been realized experimentally.
    Keywords: K-paracelsiandense double-crankshaft zeolite topologiesstructure refinementcrystal engineeringinorganic porous solidsmicroporous materials
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2018-02-21
    Description: Cytochrome bc1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
    Keywords: cryo-electron microscopycryo-EMmembrane proteinselectron-transport chainmalariacytochrome bc1
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-03-06
    Keywords: crystallographytherapeutic medicinesstructure-guided drug developmenteditorial
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 4
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-03-06
    Keywords: diffuse scatteringintermolecular correlationsLLM models
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 5
    Publication Date: 2018-09-15
    Description: It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.
    Keywords: coherent diffractive imagingsignal-to-noise ratiospatial resolutioninformation capacity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2018-09-19
    Description: The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.
    Keywords: single-particle imagingthree-dimensional virus reconstructionsXFELs
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 7
    Publication Date: 2018-09-13
    Description: This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization. This method can be expanded to any small-molecule-driven protein reaction with conformational changes traceable by X-ray scattering where the small molecule can be photocaged.
    Keywords: biophysicsX-ray solution scatteringphotocagingstructural biology
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 8
    Publication Date: 2018-10-30
    Description: A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds. Herein, the focus is on the formation energy, lattice parameter and Curie temperature of the examined materials. Based on the information obtained on the similarities between the materials, a hierarchical clustering technique is applied to learn the cluster structures of the materials that facilitate interpretation of the mechanism, and an improvement in the regression models is introduced to predict the physical properties of the materials. The experiments show that rational and meaningful group structures can be obtained and that the prediction accuracy of the materials' physical properties can be significantly increased, confirming the rationality of the proposed similarity measure.
    Keywords: data miningmaterials informaticsfirst-principles calculationsphysical properties of materialsmachine learningsimilarity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 9
    Publication Date: 2018-10-30
    Description: The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O—H...O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzophenone moieties bound by C—H...π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.
    Keywords: ketoprophencharge densitycrystal structurespharmaceuticalsbioinversion
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 10
    Publication Date: 2018-10-30
    Description: Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different `cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention. In order to overcome these limitations, a deep learning-based algorithm named Deep Consensus is presented in this work. Deep Consensus works by computing a smart consensus over the output of different particle-picking algorithms, resulting in a set of particles with a lower false-positive ratio than the initial set obtained by the pickers. Deep Consensus is based on a deep convolutional neural network that is trained on a semi-automatically generated data set. The performance of Deep Consensus has been assessed on two well known experimental data sets, virtually eliminating user intervention for pruning, and enhances the reproducibility and objectivity of the whole process while achieving precision and recall figures above 90%.
    Keywords: cryo-EMdeep learningimage processingparticle pruningthree-dimensional reconstruction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 11
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 12
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-11-09
    Description: Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
    Keywords: electron cryo-microscopysignal detectionfalse discovery ratecryo-EM densitysubtomogram averaginglocal resolutionligand binding
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 13
    Publication Date: 2018-10-12
    Description: The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported. Here, solution structures of full-length GluA2 are reported using small-angle neutron scattering (SANS) with a novel, fully matched-out detergent. The GluA2 solution structure was investigated in the resting state as well as in the presence of AMPA and of the negative allosteric modulator GYKI-53655. In solution and at neutral pH, the SANS data clearly indicate that GluA2 is in a compact form in the resting state. The solution structure resembles the crystal structure of GluA2 in the resting state, with an estimated maximum distance (Dmax) of 179 ± 11 Å and a radius of gyration (Rg) of 61.9 ± 0.4 Å. An ab initio model of GluA2 in solution generated using DAMMIF clearly showed the individual domains, i.e. the extracellular N-terminal domains and ligand-binding domains as well as the transmembrane domain. Solution structures revealed that GluA2 remained in a compact form in the presence of AMPA or GYKI-53655. At acidic pH only, GluA2 in the presence of AMPA adopted a more open conformation of the extracellular part (estimated Dmax of 189 ± 5 Å and Rg of 65.2 ± 0.5 Å), resembling the most open, desensitized class 3 cryo-EM structure of GluA2 in the presence of quisqualate. In conclusion, this methodological study may serve as an example for future SANS studies on membrane proteins.
    Keywords: ionotropic glutamate receptorsmall-angle neutron scatteringagonistsnegative allosteric modulatorsresting stateAlzheimer's diseaseParkinson's diseaseepilepsy
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 14
    Publication Date: 2018-10-18
    Description: This study investigated the structural and magnetic properties of Mn3−xFexGa alloys (x = 0, 0.2, 0.4, 0.6, 0.8, 1) under different heat-treatment conditions. A tetragonal structure was observed in samples that were heat treated at 623 K for three days followed by quenching in ice water. These tetragonal alloys present large coercive fields in the range 0.8–5 kOe and low saturation magnetization, and have great potential for application in spin-transfer torque-based devices. A hexagonal structure was observed in samples subjected to heat treatment at 883 K for three days following quenching in ice water. A moderate decrease in the coercive field has been observed for the hexagonal alloys compared with those with a tetragonal structure. However, the Mn3−xFexGa alloys with a hexagonal structure exhibit other attractive magnetic properties, including collinear and non-collinear magnetic properties, holding high promise for technological applications. A face-centred-cubic (f.c.c.) structure was observed when subjected to annealing at 1073 K for three days followed by quenching in ice water. In contrast to the tetragonal and hexagonal structures, all f.c.c. alloys exhibit antiferromagnetic behaviour. This versatile material can display a wide range of multi-functionalities attributed to its tuneable crystal structure. This investigation will guide the design of multiple structures of these materials in order to utilise the wide functionalities for practical applications.
    Keywords: Mn–Fe–Ga alloystetragonal Heusler alloysmultiple structural materials
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 15
    Publication Date: 2018-10-20
    Description: The application of X-ray photon correlation spectroscopy (XPCS) at free-electron laser (FEL) facilities enables, for the first time, the study of dynamics on a (sub-)nanometre scale in an unreached time range between femtoseconds and seconds. For soft-matter materials, radiation damage is a major limitation when going beyond single-shot applications. Here, an XPCS study is presented at a hard X-ray FEL on radiation-sensitive polymeric poly(N-isopropylacrylamide) (PNIPAM) nanoparticles. The dynamics of aqueous suspensions of densely packed silica-PNIPAM core-shell particles and a PNIPAM nanogel below the radiation-damage threshold are determined. The XPCS data indicate non-diffusive behaviour, suggesting ballistic and stress-dominated heterogeneous particle motions. These results demonstrate the feasibility of XPCS experiments on radiation-sensitive soft-matter materials at FEL sources and pave the way for future applications at MHz repetition rates as well as ultrafast modes using split-pulse devices.
    Keywords: XPCSFELPNIPAM nanoparticlesSACLAradiation-damage thresholdsoft-matter materials
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 16
    Publication Date: 2018-11-13
    Description: Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump–probe experiments.
    Keywords: free-electron lasersserial femtosecond crystallographymembrane proteinstwo-dimensional crystals
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 17
    Publication Date: 2018-11-19
    Description: β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.
    Keywords: bioinformaticsprotein structurecomputational modellingmolecular simulationstructural biologyWD40 proteinsβ-propeller proteins
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 18
    Publication Date: 2018-11-30
    Description: Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH22+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitrogen. The linking hydrogen bonds are approximately perpendicular to the anion–water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,−1) bond critical points. Weaker interactions between the PyBIGH22+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.
    Keywords: carbon captureguanidineX-ray diffractionneutron diffractioncharge densitytopological analysiscrystal engineeringintermolecular interactionshydrogen bondingenvironmental chemistry
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 19
    Publication Date: 2018-12-08
    Description: Metal–organic frameworks with highly ordered porosity have been studied extensively. In this paper, the effect of framework (pore) disorder on the gas sorption of azole-based isoreticular Cu(II) MOFs with rtl topology and characteristic 1D tubular pore channels is investigated for the first time. In contrast to other isoreticular rtl metal–organic frameworks, the Cu(II) metal–organic framework based on 5-(1H-imidazol-1-yl)isophthalate acid has a crystallographically identifiable disordered framework without open N-donor sites. The framework provides a unique example for investigating the effect of pore disorder on gas sorption that can be systematically evaluated. It exhibits remarkable temperature-dependent hysteretic CO2 sorption up to room temperature, and shows selectivity of CO2 over H2, CH4 and N2 at ambient temperature. The unique property of the framework is its disordered structure featuring distorted 1D tubular channels and DMF-guest-remediated defects. The results imply that structural disorder (defects) may play an important role in the modification of the performance of the material.
    Keywords: metal–organic frameworksT-shaped ligandsdisorderMOFssolid propertieschannel structuresgas separation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 20
    Publication Date: 2018-12-08
    Description: SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
    Keywords: serial crystallographyX-ray free-electron lasersXFELelectron diffractiondiffract-then-destroydynamical studiesauto-indexing algorithmsBragg peaks
    Electronic ISSN: 2052-2525
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  • 21
    Publication Date: 2018-03-23
    Description: The epoxide hydrolase StEH1 catalyzes the hydrolysis of trans-methylstyrene oxide to 1-phenylpropane-1,2-diol. The (S,S)-epoxide is exclusively transformed into the (1R,2S)-diol, while hydrolysis of the (R,R)-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure–activity analysis using the available crystal structures of all tested enzyme variants. Finally, empirical valence-bond simulations were performed in order to provide additional insight into the observed kinetic behaviour and ratios of the diol product enantiomers. These combined data allow us to present a model for the flux through the catalyzed reactions. With the (R,R)-epoxide, ring opening may occur at either C atom and with similar energy barriers for hydrolysis, resulting in a mixture of diol enantiomer products. However, with the (S,S)-epoxide, although either epoxide C atom may react to form the covalent enzyme intermediate, only the pro-(R,S) alkylenzyme is amenable to subsequent hydrolysis. Previously contradictory observations from kinetics experiments as well as product ratios can therefore now be explained for this biocatalytically relevant enzyme.
    Keywords: epoxide hydrolasestereoselectivityempirical valence-bond simulationsbiocatalysisreaction fluxtrans-methylstyrene oxide
    Electronic ISSN: 2052-2525
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  • 22
    Publication Date: 2018-03-23
    Description: High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate `structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a `top-hat' geometry, which was rapidly transformed to a `side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.
    Keywords: serial crystallographycopper nitrite reductasevariable temperatureradiolysisstructural dynamicsdensity functional theory
    Electronic ISSN: 2052-2525
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  • 23
    Publication Date: 2018-01-20
    Description: To understand the main properties of cement, a ubiquitous material, a sound description of its chemistry and mineralogy, including its reactivity in aggressive environments and its mechanical properties, is vital. In particular, the porosity distribution and associated sample carbonation, both of which affect cement's properties and durability, should be quantified accurately, and their kinetics and mechanisms of formation known both in detail and in situ. However, traditional methods of cement mineralogy analysis (e.g. chemical mapping) involve sample preparation (e.g. slicing) that can be destructive and/or expose cement to the atmosphere, leading to preparation artefacts (e.g. dehydration). In addition, the kinetics of mineralogical development during hydration, and associated porosity development, cannot be examined. To circumvent these issues, X-ray diffraction computed tomography (XRD-CT) has been used. This allowed the mineralogy of ternary blended cement composed of clinker, fly ash and blast furnace slag to be deciphered. Consistent with previous results obtained for both powdered samples and dilute systems, it was possible, using a consolidated cement paste (with a water-to-solid ratio akin to that used in civil engineering), to determine that the mineralogy consists of alite (only detected in the in situ hydration experiment), calcite, calcium silicate hydrates (C-S-H), ettringite, mullite, portlandite, and an amorphous fraction of unreacted slag and fly ash. Mineralogical evolution during the first hydration steps indicated fast ferrite reactivity. Insights were also gained into how the cement porosity evolves over time and into associated spatially and time-resolved carbonation mechanisms. It was observed that macroporosity developed in less than 30 h of hydration, with pore sizes reaching about 100–150 µm in width. Carbonation was not observed for this time scale, but was found to affect the first 100 µm of cement located around macropores in a sample cured for six months. Regarding this carbonation, the only mineral detected was calcite.
    Keywords: cementsynchrotron radiationX-ray diffraction tomographycarbonationporositycalcite
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 24
    Publication Date: 2018-01-26
    Description: The crystal structure of the excitonic insulator Ta2NiSe5 has been investigated under a range of pressures, as determined by the complementary analysis of both single-crystal and powder synchrotron X-ray diffraction measurements. The monoclinic ambient-pressure excitonic insulator phase II transforms upon warming or under a modest pressure to give the semiconducting C-centred orthorhombic phase I. At higher pressures (i.e. 〉3 GPa), transformation to the primitive orthorhombic semimetal phase III occurs. This transformation from phase I to phase III is a pressure-induced first-order phase transition, which takes place through coherent sliding between weakly coupled layers. This structural phase transition is significantly influenced by Coulombic interactions in the geometric arrangement between interlayer Se ions. Furthermore, upon cooling, phase III transforms into the monoclinic phase IV, which is analogous to the excitonic insulator phase II. Finally, the excitonic interactions appear to be retained despite the observed layer sliding transition.
    Keywords: inorganic materialshigh-pressure single-crystal X-ray diffractionexcitonic insulators
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 25
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-01-26
    Description: Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.
    Keywords: diffuse scatteringprotein crystallographyX-ray diffractionmolecular-dynamics simulationprotein conformational ensemblestaphylococcal nucleaseX-ray crystallographymolecular crystalsmolecular simulation
    Electronic ISSN: 2052-2525
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  • 26
    facet.materialart.
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-02-22
    Description: Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.
    Keywords: diffuse scatteringintermolecular correlations
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 27
    Publication Date: 2018-02-23
    Description: The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are `stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein. This molecular mechanism has been demonstrated previously for the endonuclease of the prototype Lymphocytic choriomeningitis virus (LCMV). However, the mode of action of this enzyme is not fully understood as the original structure did not contain catalytic metal ions. The pivotal role played by the cap-snatching process in the life cycle of the virus and the highly conserved nature of the endonuclease domain make it a target of choice for the development of novel antiviral therapies. Here, the binding affinities of two diketo-acid (DKA) compounds (DPBA and L-742,001) for the endonuclease domain of LCMV were evaluated using biophysical methods. X-ray structures of the LCMV endonuclease domain with catalytic ions in complex with these two compounds were determined, and their efficacies were assessed in an in vitro endonuclease-activity assay. Based on these data and computational simulation, two new DKAs were synthesized. The LCMV endonuclease domain exhibits a good affinity for these DKAs, making them a good starting point for the design of arenavirus endonuclease inhibitors. In addition to providing the first example of an X-ray structure of an arenavirus endonuclease incorporating a ligand, this study provides a proof of concept that the design of optimized inhibitors against the arenavirus endonuclease is possible.
    Keywords: ArenaviridaeendonucleasesLymphocytic choriomeningitis virusLCMVdiketo acidscompound optimizationmetal chelation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 28
    Publication Date: 2018-07-21
    Description: Heterogeneous catalysts are of great interest in many industrial processes for environmental reasons and, during recent years, a great effort has been devoted to obtain metal–organic frameworks (MOFs) with improved catalytic behaviour. Few supramolecular metal–organic frameworks (SMOFs) are stable under ambient conditions and those with anchored catalysts exhibit favourable properties. However, this paper presents an innovative approach that consists of using metal nodes as both structural synthons and catalysts. Regarding the latter, metalloporphyrins are suitable candidates to play both roles simultaneously. In fact, there are a number of papers that report coordination compounds based on metalloporphyrins exhibiting these features. Thus, the aim of this bioinspired work was to obtain stable SMOFs (at room temperature) based on metalloporphyrins and explore their catalytic activity. This work reports the environmentally friendly microwave-assisted synthesis and characterization of the compound [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O (TPPS = meso-tetraphenylporphine-4,4′,4′′,4′′′-tetrasulfonic acid and bipy = 4,4′-bipyridine). This compound is the first example of an MnTPPS-based SMOF, as far as we are aware, and has been structurally and thermally characterized through single-crystal X-ray diffraction, IR spectroscopy, thermogravimetry and transmission electron microscopy. Additionally, this work explores not only the catalytic activity of this compound but also of the compounds μ-O-[FeTCPP]2·16DMF and [CoTPPS0.5(bipy)(H2O)2]·6H2O. The structural features of these supramolecular materials, with accessible networks and high thermal stability, are responsible for their excellent behaviour as heterogeneous catalysts for different oxidation, condensation (aldol and Knoevenagel) and one-pot cascade reactions.
    Keywords: metalloporphyrinssupramolecular MOFsheterogeneous catalystsKnoevenagel condensationsaldol condensationsone-pot cascade reactions
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 29
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-07-28
    Description: The hypothesis that H/D exchange affects the structural formation of organic compounds in the solid state is supported by a deeper understanding of the altering polymorphism of ROY (a substance striking for its high number of polymorphic forms) through deuteration. Therefore, ROY was deuterated at its amine function, which leads to a seemingly small yet effective modification of the hydrogen-bond strength. In contrast to the crystallization of the non-deuterated ROY in methanol or ethanol, which leads to the simultaneous formation of two forms (OP and Y polymorphs), so-called concomitant polymorphs, the crystallization of d1-ROY leads to the selective formation of the Y polymorph exclusively. The preferred aggregation behavior of the Y form of d1-ROY is assigned to the weakening of an intramolecular hydrogen bond and a consequently strengthened intermolecular hydrogen bond after deuteration.
    Keywords: concomitant polymorphsdeuterationhydrogen bondsROYcrystal engineeringH/D exchange
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 30
    Publication Date: 2018-07-28
    Description: Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.
    Keywords: X-ray free-electron lasersFELsX-ray FEL pulse trainsmegahertz repetition rates
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 31
    Publication Date: 2018-07-31
    Description: The recent paper by Belo, Pereira, Freire, Argyriou, Eckert & Bordallo [(2018), IUCrJ, 5, 6–12] reports observations that may lead one to think of very strong and visible consequences of the parity-violation energy difference between enantiomers of a molecule, namely alanine. If proved, this claim would have an enormous impact for research in structural chemistry. However, alternative, more realistic, explanations of their experiments have not been ruled out by the authors. Moreover, the theoretical calculations carried out to support the hypothesis are unable to differentiate between enantiomers (molecules or crystals). Therefore, the conclusions drawn by Belo et al. (2018) are deemed inappropriate as the data presented do not contain sufficient information to reach such a conclusion.
    Keywords: parity-violation energyenantiomersphase transitionsamino acids
    Electronic ISSN: 2052-2525
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  • 32
    Publication Date: 2018-05-30
    Description: Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
    Keywords: SAXSDAMMIXintermediatesmacromolecular solutionsbiological processes
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 33
    Publication Date: 2018-06-26
    Description: An error in the paper by Pflüger, Soltwisch, Probst, Scholze & Krumrey [IUCrJ (2017), 431–438] is corrected.
    Keywords: grazing-incidence small-angle X-ray scatteringGISAXSbeam footprintlithographic inspectiongratings
    Electronic ISSN: 2052-2525
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  • 34
    Publication Date: 2018-06-26
    Description: Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.
    Keywords: Mycobacterium tuberculosismethionyl-tRNA synthetasecrystal structureinduced fitantituberculosis drugs
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 35
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-06-26
    Description: Synchrotron single-crystal X-ray diffraction has revealed diffuse scattering alongside sharp satellite reflections for different samples of mullite (Al4+2xSi2−2xO10−x). Structural models have been developed in (3+1)-dimensional superspace that account for vacancy ordering and Al/Si ordering based on harmonic modulation functions. A constraint scheme is presented which explains the crystal-chemical relationships between the split sites of the average structure. The modulation amplitudes of the refinements differ significantly by a factor of ∼3, which is explained in terms of different degrees of ordering, i.e. vacancies follow the same ordering principle in all samples but to different extents. A new approach is applied for the first time to determine Al/Si ordering by combining density functional theory with the modulated volumes of the tetrahedra. The presence of Si–Si diclusters indicates that the mineral classification of mullite needs to be reviewed. A description of the crystal structure of mullite must consider both the chemical composition and the degree of ordering. This is of particular importance for applications such as advanced ceramics, because the physical properties depend on the intrinsic structure of mullite.
    Keywords: Al/Si orderingvacancy orderingceramicssuperspaceincommensurate structures
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 36
    facet.materialart.
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-06-26
    Description: There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase (RpNiR) with nitric oxide (NO) (−0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT97. Remarkably, the structure of a catalytic copper-deficient enzyme also shows Tyr323 in the closed position despite the absence of type 2 copper (T2Cu), clearly demonstrating that the status of Tyr323 is not controlled by T2Cu or its redox chemistry. It is also shown that the activation by NO is not through binding to haem. It is proposed that activation of the Tyr323 switch is controlled by NO through proton abstraction from tyrosine and the formation of HNO. The insight gained here for the use of tyrosine as a switch in catalysis has wider implications for catalysis in biology.
    Keywords: catalysisredox biologystructural biologyenzyme mechanismdenitrificationnitrogen cyclecopper-haem nitrite reductasesRalstonia pickettii
    Electronic ISSN: 2052-2525
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  • 37
    Publication Date: 2018-06-26
    Description: Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N...I halogen bonding – a `workhorse' interaction for the crystal engineer – to support a single-crystal-to-single-crystal [2+2] photodimerization. A comparison is provided of the geometric changes experienced by the halogen-bonded components in the single-crystal reaction to the current crystal landscape of N...I halogen bonds, as derived from the Cambridge Structural Database. Specifically, a linear-to-bent type of deformation of the halogen-bonded components was observed, which is expected to support the development of functional halogen-bonded materials containing molecules that can undergo movements in close-packed crystal environments.
    Keywords: solid-state reactivityhalogen bondsphotodimerizationsupramolecular chemistrysingle-crystal-to-single-crystal reactioncrystal engineeringco-crystalsorganic solid-state reactionsframework-structured solids and amorphous materialsmolecular crystals
    Electronic ISSN: 2052-2525
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  • 38
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-05-12
    Description: X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable Rwork/Rfree. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.
    Keywords: FSEARCHIPCASiterative phasingcryo-EMmodel buildingstructure determinationcryo-electron microscopyX-ray crystallographyphase problem
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 39
    facet.materialart.
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-06-02
    Description: Cryo-electron microscopy (cryo-EM) directly images the distribution of electrostatic potential (ESP) within macromolecules, and thus can provide much more information about atomic charge than X-ray crystallography. The electron-scattering length of an isolated ion is quite different from that of the corresponding neutral atom. The difference is very large at small scattering angles where the effects of electron distributions are largest, but becomes smaller at high scattering angles where nuclear charge determines outcomes. For this reason, in cryo-EM maps that have been solved at resolutions lower than ∼2.5 Å, peaks corresponding to anions will always be less prominent than those of cations, and may even be negative. Furthermore, if a map of this kind is smeared computationally after the fact, which reduces its effective resolution, anion peaks will diminish in size, cation peaks will grow and peaks that represent uncharged atoms will remain about the same. These effects can be used to determine the sign of the charges carried by the ions associated with a macromolecule and even estimate their magnitudes. The ESP value for a cation in a cation–anion pair is smaller than the value of the cation in isolation, but the ESP value for the anion in the ionic pair is greater than the value of the anion in isolation. The experimental range of ESP values for Mg2+ relative to that of the closest C1′ atom is found to be between 0.57 and 1.27.
    Keywords: cryo-EMelectron-scattering lengthtransition B factorMott equationribosome
    Electronic ISSN: 2052-2525
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  • 40
    Publication Date: 2018-06-07
    Description: The protein Pgp3 is implicated in the sexually transmitted disease chlamydia and comprises an extended complex arrangement of a C-terminal domain (CTD) and an N-terminal domain (NTD) linked by a triple-helix coiled coil (THCC). Here, the X-ray crystal structure of Pgp3 from an LGV1 strain is reported at the highest X-ray diffraction resolution obtained to date for the full protein. The protein was crystallized using a high concentration of potassium bromide, which resulted in a new crystal form with relatively low solvent content that diffracted to a resolution of 1.98 Å. The three-dimensional structure of this new crystal form is described and compared with those of other crystal forms, and the potassium bromide binding sites and the relevance to chlamydia isolates from around the globe are described. The crystal packing is apparently driven by the CTDs. Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTD via crystal packing. The key avenue to resolving these oddities in the crystal structure analysis was a complete new analysis in space group P1 and determining the space group as P212121. This space-group assignment was that originally determined from the diffraction pattern but was perhaps complicated by translational noncrystallographic symmetry. This crystal structure of a three-domain multi-macromolecular complex with two misaligned threefold axes was a unique challenge and has not been encountered before. It is suggested that a specific intermolecular interaction, possibly of functional significance in receptor binding in chlamydia, might allow the design of a new chemotherapeutic agent against chlamydia.
    Keywords: chlamydia proteinPgp3crystallizationcrystal formprotein structureX-ray crystallographystructural biologysexually transmitted diseases
    Electronic ISSN: 2052-2525
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  • 41
    Publication Date: 2018-06-09
    Description: This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium–cytosinium trans sugar/sugar edge pair and an adeninium–adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation–cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
    Keywords: charge densitymultipole refinementquantum crystallographyelectrostatic potentialelectrostatic interaction energylike-charged ionsnucleobasescytosineadenineguaninebase pairsintermolecular interactionsspin densitymomentum densityhydrogen bondingpharmaceutical solidsnucleic acid structures
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 42
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-04-20
    Description: Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure with C2221 symmetry) and OP (orthorhombic structure with P212121 symmetry)-like structures appeared in sequence. In contrast, the latter process showed that MX1, OP, OC, LHP and HP-like structures appeared in sequence. Detailed analysis of the calculated structures showed that the configuration underwent stepwise changes associated with several characteristic modes. First, the structure of HP-tridymite determined from diffraction experiments was identified as a time-averaged structure in a similar manner to β-cristobalite, thus indicating the important role of floppy modes of oxygen atoms at high temperature – one of the common features observed in silica crystals and glass. Secondly, the main structural changes were ascribed to a combination of distortion of the six-membered rings in the layers and misalignment between layers. We suggest that the slowing down of floppy oxygen movement invokes the multistage emergence of structures with lower symmetry on cooling. This study therefore not only reproduces the sequence of the main polymorphic transitions in tridymite, except for the appearance of the monoclinic phase, but also explains the microscopic dynamic structural changes in detail.
    Keywords: silicatridymitemolecular dynamicsstructurephase transitionspolymorphs
    Electronic ISSN: 2052-2525
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  • 43
    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
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  • 44
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-01-04
    Keywords: functional materialsstructural scienceeditorial
    Electronic ISSN: 2052-2525
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  • 45
    Publication Date: 2018-01-11
    Description: Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.
    Keywords: protein crystalsstatic disorderdynamic disorderconformational entropyelastic molecular shapeoscillating crystal latticelocal entropic forceX-ray crystallographycrystallizationcrystal growth
    Electronic ISSN: 2052-2525
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  • 46
    Publication Date: 2018-01-11
    Description: Knowledge of the interactions between nanomaterials and large-size mammalian cells, including cellular uptake, intracellular localization and translocation, has greatly advanced nanomedicine and nanotoxicology. Imaging techniques that can locate nanomaterials within the structures of intact large-size cells at nanoscale resolution play crucial roles in acquiring this knowledge. Here, the quantitative imaging of intracellular nanomaterials in three dimensions was performed by combining dual-energy contrast X-ray microscopy and an iterative tomographic algorithm termed equally sloped tomography (EST). Macrophages with a size of ∼20 µm that had been exposed to the potential antitumour agent [Gd@C82(OH)22]n were investigated. Large numbers of nanoparticles (NPs) aggregated within the cell and were mainly located in phagosomes. No NPs were observed in the nucleus. Imaging of the nanomedicine within whole cells advanced the understanding of the high-efficiency antitumour activity and the low toxicity of this agent. This imaging technique can be used to probe nanomaterials within intact large-size cells at nanometre resolution uniformly in three dimensions and may greatly benefit the fields of nanomedicine and nanotoxicology.
    Keywords: cellular imagingX-ray tomographyequally sloped tomographydual-energy contrastcomputed tomographynanoscienceX-ray microscopyimagingstructure determination
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 47
    Publication Date: 2018-01-26
    Description: Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG–SecA complex data set. All of the models were automatically built by the method to Rfree values of between 28.9 and 39.9% and were free from the initial model bias.
    Keywords: low resolutionX-ray crystallographysingle-wavelength anomalous diffractionmultivariate statisticsmodel biasstructure determinationmembrane proteinsrefinementmulti-protein complexes
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 48
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-01-26
    Description: With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components.
    Keywords: phase transitionspolymorphshydratescocrystalsCambridge Structural Database
    Electronic ISSN: 2052-2525
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  • 49
    Publication Date: 2018-02-15
    Description: Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.
    Keywords: EIGERhybrid pixel detectorselectron crystallographySAPO-34
    Electronic ISSN: 2052-2525
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  • 50
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-01-04
    Keywords: carbonic anhydrase IIproton transferwater dynamicshigh pressure
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 51
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    facet.materialart.
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-12-19
    Description: The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph. The types of defect generated in the deformation of a face-centered cubic crystal are analyzed through the deformation pathway graph and compared with experimental observations.
    Keywords: crystal deformationcrystalline defectsgroup theoryCayley graph
    Electronic ISSN: 2052-2525
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  • 52
    facet.materialart.
    facet.materialart.
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-12-19
    Description: The defect structure of γ-Al2O3 derived from boehmite was investigated using a combination of selected-area electron diffraction (SAED) and powder X-ray diffraction (XRD). Both methods confirmed a strong dependence of the diffraction line broadening on the diffraction indices known from literature. The analysis of the SAED patterns revealed that the dominant structure defects in the spinel-type γ-Al2O3 are antiphase boundaries located on the lattice planes (00l), which produce the sublattice shifts {{1}\over{4}}\langle 10{\overline 1}\rangle. Quantitative information about the defect structure of γ-Al2O3 was obtained from the powder XRD patterns. This includes mainly the size of γ-Al2O3 crystallites and the density of planar defects. The correlation between the density of the planar defects and the presence of structural vacancies, which maintain the stoichiometry of the spinel-type γ-Al2O3, is discussed. A computer routine running on a fast graphical processing unit was written for simulation of the XRD patterns. This routine calculates the atomic positions for a given kind and density of planar defect, and simulates the diffracted intensities with the aid of the Debye scattering equation.
    Keywords: γ-aluminamicrostructure defectsantiphase boundariesrotational boundariesselected-area electron diffractionpowder X-ray diffractionDebye equationanisotropic broadening
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  • 53
    Publication Date: 2018-12-19
    Description: The present article is devoted to the characterization of the structural phase transitions of the [CH3NH3][Co(COOH)3] (1) perovskite-like metal–organic compound through variable-temperature single-crystal neutron diffraction. At room temperature, compound 1 crystallizes in the orthorhombic space group Pnma (phase I). A decrease in temperature gives rise to a first phase transition from the space group Pnma to an incommensurate phase (phase II) at approximately 128 K. At about 96 K, this incommensurate phase evolves into a second phase with a sharp change in the modulation vector (phase III). At lower temperatures (ca 78 K), the crystal structure again becomes commensurate and can be described in the monoclinic space group P21/n (phase IV). Although phases I and IV have been reported previously [Boča et al. (2004). Acta Cryst. C60, m631–m633; Gómez-Aguirre et al. (2016). J. Am. Chem. Soc. 138, 1122–1125; Mazzuca et al. (2018). Chem. Eur. J. 24, 388–399], phases III and IV corresponding to the Pnma(00γ)0s0 space group have not yet been described. These phase transitions involve not only the occurrence of small distortions in the three-dimensional anionic [Co(HCOO)3]− framework, but also the reorganization of the [CH3NH3]+ counter-ions in the cavities of the structure, which gives rise to an alteration of the hydrogen-bonded network, modifying the electrical properties of compound 1.
    Keywords: phase transitionsincommensurate structuresformate ligandmultiferroic materialsaperiodic structuresmaterials scienceinorganic chemistryphase transitionsMOFs
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  • 54
    Publication Date: 2018-07-31
    Keywords: chiralitystructure analysisconfigurational changephase transitionsintermolecular interactionsamino acids
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  • 55
    Publication Date: 2018-08-09
    Description: The natural sII-type clathrasil chibaite [chemical formula SiO2·(M12,M16), where Mx denotes a guest molecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group Fd{\overline 3}m [V = 7348.9 (17) Å3, a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning. The intensities of weak superstructure reflections increase as temperature decreases. A monoclinic twinned superstructure was derived at 100 K [A2/n, V = 7251.0 (17) Å3, a′ = 23.7054 (2), b′ = 13.6861 (11), c′ = 23.7051 (2) Å, β′ = 109.47°]. The transformation matrix from the cubic to the monoclinic system is ai′ = (½ 1 ½ / ½ 0 −½ / ½ −1 ½). The A2/n host framework has Si—O bond lengths and Si—O—Si angles that are much closer to known values for stable silicate-framework structures compared with the averaged Fd{\overline 3}m model. As suggested from band splitting observed in the Raman spectra, the [512]-type cages (one crystallographically unique in Fd{\overline 3}m, four different in A2/n) entrap the hydrocarbon species (CH4, C2H6, C3H8, i-C4H10). The [51264]-type cage was found to be unique in both structure types. It contains the larger hydrocarbon molecules C2H6, C3H8 and i-C4H10.
    Keywords: chibaiteclathrasilshydrocarbonsRaman spectroscopyX-ray diffractionlow temperature
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  • 56
    Publication Date: 2018-08-09
    Description: Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and `graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
    Keywords: loop buildingstructural re-buildingPDB-REDOmodel completioncrystallography
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  • 57
    Publication Date: 2018-08-30
    Description: Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
    Keywords: phytochromesphotoreceptorsphotosynthetic bacteriamyxobacteriaabsorption spectra
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  • 58
    Publication Date: 2018-09-15
    Description: This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form IIHT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the IIHT form undergoes two further (reversible) phase transitions upon cooling at 361 K (IIRT) and 181 K (IILT). All three phases (forms IIHT, IIRT and IILT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term `conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.
    Keywords: molecular crystalspolymorphismphase transitionsconformational changesenergy minimization
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  • 59
    Publication Date: 2018-09-13
    Description: Hexaferrites are an important class of magnetic oxides with applications in data storage and electronics. Their crystal structures are highly modular, consisting of Fe- or Ba-rich close-packed blocks that can be stacked in different sequences to form a multitude of unique structures, producing large anisotropic unit cells with lattice parameters typically 〉100 Å along the stacking axis. This has limited atomic-resolution structure solutions to relatively simple examples such as Ba2Zn2Fe12O22, whilst longer stacking sequences have been modelled only in terms of block sequences, with no refinement of individual atomic coordinates or occupancies. This paper describes the growth of a series of complex hexaferrite crystals, their atomic-level structure solution by high-resolution synchrotron X-ray diffraction, electron diffraction and imaging methods, and their physical characterization by magnetometry. The structures include a new hexaferrite stacking sequence, with the longest lattice parameter of any hexaferrite with a fully determined structure.
    Keywords: large repeat hexaferritesmixed-layer structural modelspolytypesstacking sequencesdefectsmagnetic properties
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  • 60
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-10-09
    Description: Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace `guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.
    Keywords: crystallographic phase problemthree-phase invariantsconvergent-beam electron diffractionstructure determinationenantiomorph ambiguitynanocrystalsdynamical studiesmultiple scattering
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  • 61
    Publication Date: 2018-10-11
    Description: Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively. To gain further insight into oligomer-assembly mechanisms as well as into Goodpasture's and Alport's syndromes, crystal structures of noncollagenous domains produced by recombinant methods were determined. The spontaneous formation of canonical homohexamers (dimers of trimers) of these domains of the α1, α3 and α5 chains was shown and the components of the Goodpasture's disease epitopes were viewed. Crystal structures of the α2 and α4 noncollagenous domains generated by recombinant methods were also determined. These domains spontaneously form homo-oligomers that deviate from the canonical architectures since they have a higher number of subunits (dimers of tetramers and of hexamers, respectively). Six flexible structural motifs largely explain the architectural variations. These findings provide insight into noncollagenous domain folding, while supporting the in vivo operation of extrinsic mechanisms for restricting the self-assembly of noncollagenous domains. Intriguingly, Alport's syndrome missense mutations concentrate within the core that nucleates the folding of the noncollagenous domain, suggesting that this syndrome, when owing to missense changes, is a folding disorder that is potentially amenable to pharmacochaperone therapy.
    Keywords: collagen type IVnetwork assembly(IV)NC1 hexamersGoodpasture's diseaseAlport's syndrome
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  • 62
    Publication Date: 2018-07-21
    Description: In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand–maximize–compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
    Keywords: X-ray serial microcrystallographysparse dataEMC algorithmprotein microcrystallographystorage-ring synchrotron sources
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  • 63
    Publication Date: 2018-08-09
    Description: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
    Keywords: serial crystallographySIRAS phasinglipidic cubic phaseheavy-atom soakingde novo protein structure determination
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  • 64
    Publication Date: 2018-08-30
    Description: The question of whether intermolecular interactions in crystals originate from localized atom...atom interactions or as a result of holistic molecule...molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby–Gould bond indices are reported for intermolecular `σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom...atom and molecule...molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the `conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom...atom interactions in the formation of these intermolecular binding motifs.
    Keywords: intermolecular interactionsbond orderionicityhydrogen bondinghalogen bondingcrystal engineeringcomputational modellingmolecular crystals
    Electronic ISSN: 2052-2525
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  • 65
    Publication Date: 2018-09-06
    Description: In this study, the nature and characteristics of a short Br...π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br...π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br...π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).
    Keywords: σ-hole bondingπ-hole bondingebselenelectron densitymolecular electrostatic potentialscrystal engineeringcharge, spin and momentum densitiescomputational modellingmolecular crystals
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  • 66
    Publication Date: 2018-09-15
    Description: X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.
    Keywords: XFELsX-ray nanocrystallographyeffective form factorionizationradiation damage
    Electronic ISSN: 2052-2525
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  • 67
    facet.materialart.
    facet.materialart.
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-10-09
    Description: Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components. This initial guess is then iteratively refined by fitting experimental GISAXS images at multiple incident angles, using the distorted-wave Born approximation (DWBA) to convert between reciprocal space and detector space. This method converges to a high-quality reconstruction for the undistorted scattering, as validated by comparing with grazing-transmission scattering data. This new method for unwarping GISAXS images will broaden the applicability of grazing-incidence techniques, allowing experimenters to inspect undistorted visualizations of their data and allowing a broader range of analysis methods to be applied to GI data.
    Keywords: X-ray scatteringGISAXSGTSAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
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  • 68
    Publication Date: 2018-10-25
    Description: Pure-phase Pb(Cd1/3Nb2/3)O3 (PCN) single crystals and ceramics with a complex perovskite structure are synthesized for the first time. The local chemical ordering in PCN has been investigated by X-ray diffraction (including diffuse scattering) and Cs-corrected transmission electron microscopy experiments. It is concluded that the PCN samples have large coherent chemical ordering regions that even extend to the long range, and the ordering model is consistent with β-type chemical ordered regions. The antiphase domain boundaries were also observed. Two dielectric anomaly peaks were found in these two types of samples, one of which indicates possible relaxor behaviour. The novel structure of the completely ordered regions and its relationship with the electrical properties make PCN a unique material for the fundamental understanding of chemically substituted perovskites.
    Keywords: chemical orderingdiffuse scatteringelectron microscopyatomic resolution EDSperovskitesdielectric permittivityrelaxors
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  • 69
    Publication Date: 2018-10-25
    Description: The single-crystal X-ray structure of a 6-component organic-salt alloy (hexanary) of naftopidil (1) (an active pharmaceutical ingredient) with benzoic acid (2) and four different hydroxy-substituted benzoic acids, i.e. salicylic acid (3), 2,3-dihydroxybenzoic acid (4), 2,4-dihydroxybenzoic acid (5) and 2,6-dihydroxybenzoic acid (6), is reported. The hexanary assembly originates from the observation that the binary salts of naftopidil with the above acids are isostructural. In addition to the 6-component solid, we also describe five 5-component, ten 4-component, and ten 3-component organic-salt alloys of naftopidil (1) with carboxylic acids (2)–(6). These alloys were obtained from different combinations of the acids with the drug. The synthetic design of the multicomponent organic alloys is based on the rationale of geometrical factors (shape and size) and chemical interactions (hydrogen bonds). The common supramolecular synthon in all these crystal structures was the cyclic N+—H...O− and O—H...O hydrogen-bonded motif of R_2^2(9) graph set between the 2-hydroxyammonium group of naftopidil and the carboxylate anion. This ionic synthon is strong and robust, directing the isostructural assembly of naftopidil with up to five different carboxylic acids in the crystal structure together with the lower-level multicomponent adducts. Solution crystallization by slow evaporation provided the multicomponent organic salts and alloys which were characterized by a combination of single-crystal X-ray diffraction, powder X-ray diffraction, NMR and differential scanning calorimetry techniques.
    Keywords: active pharmaceutical ingredientscrystal engineeringnaftopidilmulticomponent solids6-component crystalsorganic-salt alloys
    Electronic ISSN: 2052-2525
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  • 70
    Publication Date: 2018-10-30
    Description: This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg–In–Yb and Mg–In–Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈11{\overline 2}0〉α directions formed a two-dimensional planar structure, which has three variants with a {10{\overline 1}0}α habit plane and full coherence with the α-Mg matrix. This finding is important for understanding the clustering and stacking behaviors of solute atoms in condensed matter, and is expected to guide the future design of novel high-strength Mg alloys strengthened by such high-density prismatic platelets.
    Keywords: magnesium alloysprecipitationprismatic plateletsquasi-unit-cellsDFTHAADF-STEM
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  • 71
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-10-30
    Keywords: crystal engineeringcrystalscrystallography
    Electronic ISSN: 2052-2525
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  • 72
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    facet.materialart.
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-11-01
    Keywords: Rayleigh scatteringXFELsaerosol injectionsingle-particle imaging
    Electronic ISSN: 2052-2525
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  • 73
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    facet.materialart.
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-11-01
    Keywords: X-ray scatteringGISAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
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    Publication Date: 2018-11-01
    Description: Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2–26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
    Keywords: viral PARP-1-interacting proteinopen reading frame 49poly(ADP-ribose) polymerase 1murine gammaherpesvirus 68Kaposi's sarcoma-associated herpesvirusstructure determinationX-ray crystallography
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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