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Crystallographic Model (crystallographic + model)
Selected Abstractsphenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statisticsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010Pavel V. Afonine phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed. [source] Local atomic structure in tetragonal pure ZrO2 nanopowdersJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2010Leandro M. Acuña The local atomic structures around the Zr atom of pure (undoped) ZrO2 nanopowders with different average crystallite sizes, ranging from 7 to 40,nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2 nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr,O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye,Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. [source] Low-resolution structure of immunoglobulins IgG1, IgM and rheumatoid factor IgM-RF from solution X-ray scattering dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2003Vladimir V. Volkov Low-resolution structures of immunoglobulins IgG, IgM and rheumatoid factor IgM-RF in solution were analyzed using synchrotron radiation small-angle X-ray scattering and the macromolecular shapes were restored ab initio from the scattering data. The shape of IgG agrees well with the distorted Y-type crystallographic model but has a swollen appearance reflecting flexibility of the molecule in solution. The structures of pentameric IgM and IgM-RF were reconstructed assuming a five-fold symmetry. The IgM displays a flat star-like shape with observable F(ab)2 regions. The overall shape of the IgM-RF is similar to that of the IgM but with distinctly asymmetric F(ab)2 regions. This result agrees with the earlier observed functional dissimilarity of the Fab fragments in the rheumatoid factor and points to their structural dissimilarity. [source] XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysisJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2003Richard W. Strange This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein from Klebsiella pneumoniae nitrogenase (Kp1) using the 1.6,Å-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by ,0.1,Å) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo. [source] Comprehensive analysis of advanced solar cell contacts consisting of printed fine-line seed layers thickened by silver platingPROGRESS IN PHOTOVOLTAICS: RESEARCH & APPLICATIONS, Issue 2 2009D. Pysch Abstract This work presents a detailed analysis of a new two-layer process to contact industrial solar cells. However, most of the results seem to be transferable to standard screen print paste contacts. The seed layer was created by a pad or screen printer and thickened by light-induced plating (LIP) of silver. These contact structures were investigated microscopically to gain a better understanding of the observed electrical parameters. A review of the present microscopic contact formation model for flat surfaces is presented. This model was extended and applied to surfaces textured with random pyramids. This analysis has revealed two new types of silver crystallites which can be described by a crystallographic model. The dependence of the silver crystallite density on the surface doping concentration was investigated. Next, the dependence of the contact resistance on the width of the seed layer was measured showing that the contact resistivity increases with a reduction of the seed layer width. These results have been further approved by an analysis of SEM images of wet-chemically etched contacts examining the density of crystallites and the fraction of removed SiNx layer. Contact resistance RC measurements before and after LIP of silver showed surprisingly a positive influence of the plating process on RC. A detailed microscopical analysis revealed four new possible current flow paths due to the LIP of a conventional contact or a seed layer. The results led to an extension of the existing model for a screen-printed contact. Copyright © 2008 John Wiley & Sons, Ltd. [source] Validation of crystallographic models containing TLS or other descriptions of anisotropyACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2010Frank Zucker The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter-domain and other large-scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface. [source] The X-ray structure of a recombinant major urinary protein at 1.75,Å resolution.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2001A comparative study of X-ray, NMR-derived structures Major urinary proteins belong to the lipocalin family and are present in the urine of rodents as an ensemble of isoforms with pheromonal activity. The crystal structure of a recombinant mouse MUP (rMUP) was solved by the molecular-replacement technique and refined to an R factor and Rfree of 20 and 26.5%, respectively, at 1.75,Å resolution. The structure was compared with an NMR model and with a crystallographic structure of the wild-type form of the protein. The crystal structures determined in different space groups present significantly smaller conformational differences amongst themselves than in comparison with NMR models. Some, but not all, of the conformational differences between the crystal and solution structures can be explained by the influence of crystallographic contacts. Most of the differences between the NMR and X-ray structures were found in the N-terminus and loop regions. A number of side chains lining the hydrophobic pocket of the molecule are more tightly packed in the NMR structure than in the crystallographic model. Surprisingly, clear and continuous electron density for a ligand was observed inside the hydrophobic pocket of this recombinant protein. Conformation of the ligand modelled inside the density is coherent with the results of recent NMR experiments. [source] | ||||||||||