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  • International Union of Crystallography (IUCr)
  • 2010-2014  (32)
  • 1980-1984  (5,963)
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  • 11
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    Automated nucleic acid chain tracing in real time (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.
    Keywords: nucleic acid chain tracingCoot
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 12
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    Location of Cu2+ in CHA zeolite investigated by X-ray diffraction using the Rietveld/maximum entropy method (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Accurate structural models of reaction centres in zeolite catalysts are a prerequisite for mechanistic studies and further improvements to the catalytic performance. The Rietveld/maximum entropy method is applied to synchrotron powder X-ray diffraction data on fully dehydrated CHA-type zeolites with and without loading of catalytically active Cu2+ for the selective catalytic reduction of NOx with NH3. The method identifies the known Cu2+ sites in the six-membered ring and a not previously observed site in the eight-membered ring. The sum of the refined Cu occupancies for these two sites matches the chemical analysis and thus all the Cu is accounted for. It is furthermore shown that approximately 80% of the Cu2+ is located in the new 8-ring site for an industrially relevant CHA zeolite with Si/Al = 15.5 and Cu/Al = 0.45. Density functional theory calculations are used to corroborate the positions and identity of the two Cu sites, leading to the most complete structural description of dehydrated silicoaluminate CHA loaded with catalytically active Cu2+ cations.
    Keywords: CHA zeolitescatalytic activitylocation of Cu2+synchrotron powder X-ray diffractionRietveld/maximum entropy method
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 13
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    The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these `stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.
    Keywords: indexing ambiguityserial femtosecond crystallography (SFX)XFELsprotein crystallographyexpectation maximization algorithm
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 14
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    Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL) is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm). This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.
    Keywords: femtosecond pulseX-ray diffractionpolarizabilityelectron densityrate equations
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 15
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    Correlated changes in structure and viscosity during gelatinization and gelation of tapioca starch granules (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Melting of native tapioca starch granules in aqueous pastes upon heating is observed in situ using simultaneous small- and wide-angle X-ray scattering (SAXS/WAXS) and solution viscometry. Correlated structure and viscosity changes suggest closely associated amylose and amylopectin chains in the semicrystalline layers, and the release of amylose chains for enhanced solution viscosity occurs largely after melting of the semicrystalline structure. Before melting, WAXS results reveal mixed crystals of A- and B-types (∼4:1 by weight), whereas SAXS results indicate that the semicrystalline layers are composed of lamellar blocklets of ca 43 nm domain size, with polydisperse crystalline (≃7.5 nm) and amorphous (≃1.1 nm) layers alternatively assembled into a lamellar spacing of ≃8.6 nm with 20% polydispersity. Upon melting, the semicrystalline lamellae disintegrate into disperse and molten amylopectin nanoclusters with dissolved and partially untangled amylose chains in the aqueous matrix which leads to increased solution viscosity. During subsequent cooling, gelation starts at around 347 K; successively increased solution viscosity coincides with the development of nanocluster aggregation to a fractal dimension ≃2.3 at 303 K, signifying increasing intercluster association through collapsed amylose chains owing to decreased solvency of the aqueous medium with decreasing temperature.
    Keywords: tapioca starch granulesgelatinizationgelationSAXS/WAXSviscosity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 16
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    Molecular self-assembly of nylon-12 nanorods cylindrically confined to nanoporous alumina (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Molecular self-assembly of nylon-12 rods in self-organized nanoporous alumina cylinders with two different diameters (65 and 300 nm) is studied with transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD) in symmetrical reflection mode. In a rod with a 300 nm diameter, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is not clear because of weak two-dimensional confinement. In a rod with a diameter of 65 nm, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is more distinct because of strong two-dimensional confinement. For the first time, selected-area electron diffraction (SAED) is applied in a transmission electron microscope to a polymer nanorod in order to determine the hydrogen-bond sheet and lamellar orientations. Results of TEM–SAED and WAXD showed that the crystals within the rod possess the γ-form of nylon-12 and that the b axis (stem axis) of the γ-form crystals is perpendicular to the long axis of the rod. These results revealed that only lamellae with 〈h0l〉 directions are able to grow inside the nanopores and the growth of lamellae with 〈hkl〉 (k ≠ 0) directions is stopped owing to impingements against the cylinder walls. The dominant crystal growth direction of the 65 nm rod in stronger two-dimensional confinement is in between the [−201] and [001] directions due to the development of a hydrogen-bonded sheet restricted along the long axis of the rod.
    Keywords: molecular self-assemblynanorodsselected-area electron diffractioncylindrical confinement
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 17
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    Viruses and viral proteins (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes.
    Keywords: bacteriophagesgenome deliveryfusion proteinsRNA-dependent RNA polymerasesviral proteasesviral receptorsviruses
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 18
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    Contributions of charge-density research to medicinal chemistry (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug–receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug–receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
    Keywords: charge-density researchmedicinal chemistrydrug designinvariomHansen–Coppens multipole modelquantum theory of atoms in molecules
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 19
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    Capability of X-ray diffraction for the study of microstructure of metastable thin films (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Metastable phases are often used to design materials with outstanding properties, which cannot be achieved with thermodynamically stable compounds. In many cases, the metastable phases are employed as precursors for controlled formation of nanocomposites. This contribution shows how the microstructure of crystalline metastable phases and the formation of nanocomposites can be concluded from X-ray diffraction experiments by taking advantage of the high sensitivity of X-ray diffraction to macroscopic and microscopic lattice deformations and to the dependence of the lattice deformations on the crystallographic direction. The lattice deformations were determined from the positions and from the widths of the diffraction lines, the dependence of the lattice deformations on the crystallographic direction from the anisotropy of the line shift and the line broadening. As an example of the metastable system, the supersaturated solid solution of titanium nitride and aluminium nitride was investigated, which was prepared in the form of thin films by using cathodic arc evaporation of titanium and aluminium in a nitrogen atmosphere. The microstructure of the (Ti,Al)N samples under study was tailored by modifying the [Al]/[Ti] ratio in the thin films and the surface mobility of the deposited species.
    Keywords: metastable thin filmsmicrostructureX-ray diffraction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 20
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    Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein (2014)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2014-11-12
    Description: Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer–monomer interface is more extensive than that at the dimer–dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
    Keywords: transthyretinamyloid assemblyneutron crystallographydeuteration
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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