scholarly journals Large-scale comparison between the diffraction-component precision indexes favors Cruickshank’s Rfree function

2021 ◽  
pp. 76-76
Author(s):  
Sorin Avram ◽  
Cristian Neanu
Keyword(s):  
Quality Assessment ◽  
Data Base ◽  
Diffraction Data ◽  
Large Scale ◽  
Data Extraction ◽  
Protein Structures ◽  
Structural Refinement ◽  
X Ray ◽  
Average Accuracy ◽  
Atomic Coordinates

This study aims to provide a first large-scale comparison between the various diffraction-component precision index (DPI) equations, assess the applicability of the parameter, and make recommendations on DPI computation. The DPI estimates the average accuracy of atomic coordinates obtained by the structural refinement of protein diffraction data, with application in crystallography and cheminformatics. Although, Cruickshank and Blow proposed DPI equations based on R- and Rfree to calculate DPI values, these remain scarcely employed in the quality assessment of Protein Data Base (PDB) files, due to unclear data extraction protocols (to assign variables), complex equations, lack of extensive applicability studies and limited access to automated computations. In order to address these shortcomings, the entire RCSB PDB database was evaluated using Cruickshank's and Blow's R and Rfree DPI variations. Computations of 143070 X-ray structures indicate that Rfree-based DPI equations apply to 30 % more protein structures compared to R-based DPI equations, with Cruickshank Rfree-based DPI (CRF) exceeding the number of successful Blow?s Rfree-based DPI (BRF) computations. Although our results indicate that, in general, resolutions < 2 ? assure consistency among the various DPIs computations (differences <0.05 ?), we recommend the use of CRF DPI because of its wider applicability.

Structural refinement of nano BaTiO3powder using X-ray diffraction data

2004 ◽  
Vol 39 (13) ◽  
pp. 4363-4366 ◽  
Author(s):  
Yong-Il Kim ◽  
Seung-Hoon Nahm ◽  
Maeng-Joon Jung
Keyword(s):  
Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
X Ray

Preparation and crystal structure of garnet-type calcium zirconium germanate Ca4ZrGe3O12

2016 ◽  
Vol 31 (4) ◽  
pp. 292-294 ◽  
Author(s):  
V. D. Zhuravlev ◽  
A. P. Tyutyunnik ◽  
N. I. Lobachevskaya
Keyword(s):  
Crystal Structure ◽  
Unit Cell Parameter ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Cell Parameter ◽  
Polycrystalline Sample ◽  
Structural Formula ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray

A polycrystalline sample of Ca4ZrGe3O12 was synthesized using the nitrate–citrate method and heated at 850–1100 °C. Structural refinement based on X-ray powder diffraction data showed that the crystal structure is of the garnet type with a cubic unit-cell parameter [a = 12.71299(3) Å] and the space group Ia$\bar 3$d. The structural formula is presented as Ca3[CaZr]octa[Ge]tetraO12.

scholarly journals Rubidium tetrafluoridobromate(III): redetermination of the crystal structure from single-crystal X-ray diffraction data

IUCrData ◽  
2019 ◽  
Vol 4 (11) ◽  
Author(s):  
Artem V. Malin ◽  
Sergei I. Ivlev ◽  
Roman V. Ostvald ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Single Crystals ◽  
Diffraction Data ◽  
Structure Type ◽  
X Ray Diffraction ◽  
X Ray ◽  
Square Planar ◽  
Atomic Coordinates

Single crystals of rubidium tetrafluoridobromate(III), RbBrF4, were grown by melting and recrystallizing RbBrF4 from its melt. This is the first determination of the crystal structure of RbBrF4 using single-crystal X-ray diffraction data. We confirmed that the structure contains square-planar [BrF4]− anions and rubidium cations that are coordinated by F atoms in a square-antiprismatic manner. The compound crystallizes in the KBrF4 structure type. Atomic coordinates and bond lengths and angles were determined with higher precision than in a previous report based on powder X-ray diffraction data [Ivlev et al. (2015). Z. Anorg. Allg. Chem. 641, 2593–2598].

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

2016 ◽  
Vol 31 (1) ◽  
pp. 71-72 ◽  
Author(s):  
Mark A. Rodriguez ◽  
Philippe E. Weck ◽  
Joshua D. Sugar ◽  
Thomas J. Kulp
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
First Principles ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Unit Cells

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

scholarly journals Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures

1998 ◽  
Vol 54 (6) ◽  
pp. 1306-1318 ◽  
Author(s):  
Christian Jelsch ◽  
Virginie Pichon-Pesme ◽  
Claude Lecomte ◽  
André Aubry
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Diffraction Data ◽  
Protein Structures ◽  
Fourier Synthesis ◽  
Covalent Bonds ◽  
X Ray ◽  
Density Peaks ◽  
Deformation Electron Density ◽  
Temperature Factors

Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (\Delta B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 Å.

scholarly journals xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

2014 ◽  
Vol 70 (9) ◽  
pp. 2344-2355 ◽  
Author(s):  
Ryan McGreevy ◽  
Abhishek Singharoy ◽  
Qufei Li ◽  
Jingfen Zhang ◽  
Dong Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Protein Structures ◽  
Data Bank ◽  
Real Space ◽  
Low Resolution ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Electron Density Map

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally,viasystematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

scholarly journals Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps

2020 ◽  
Author(s):  
Xiaogen Zhou ◽  
Yang Li ◽  
Chengxin Zhang ◽  
Wei Zheng ◽  
Guijun Zhang ◽  
...  
Keyword(s):  
Protein Structure ◽  
Large Scale ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Solution Rate ◽  
Structural Refinement ◽  
Flexible Assembly ◽  
Domain Structures ◽  
Density Maps ◽  
Domain Protein

ABSTRACTProgress in cryo-electron microscopy (cryo-EM) has provided the potential for large-size protein structure determination. However, the solution rate for multi-domain proteins remains low due to the difficulty in modeling inter-domain orientations. We developed DEMO-EM, an automatic method to assemble multi-domain structures from cryo-EM maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep neural network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to twelve continuous and discontinuous domains with medium-to-low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (TM-score >0.5) for 98% of cases and significantly outperformed the state-of-the-art methods. DEMO-EM was applied to SARS-Cov-2 coronavirus genome and generated models with average TM-score/RMSD of 0.97/1.4Å to the deposited structures. These results demonstrated an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modeling with atomic-level accuracy from cryo-EM maps.

Observations of coexistence of FCC and HCP phases in C60 by HREM

1992 ◽  
Vol 50 (1) ◽  
pp. 110-111
Author(s):  
Z.G. Li ◽  
Paul J. Fagan
Keyword(s):  
Carbon Atom ◽  
Crystalline Structure ◽  
Diffraction Data ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Neighbor Distance ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hexagonal Close Packed ◽  
Correct Structure

Since the discovery of a large scale synthesis of fullerenes there has been intense interest in the structure of these materials. The first diffraction data suggested that crystalline C60 had a hexagonal close-packed (hep) structure with a nearest neighbor distance of 10.04 Å. The possibility of a disordered stacking of C60 molecules was first noted in this study. Since then, there has been some confusion regarding the exact crystalline structure of C60 as determined by electron and X-ray diffraction. In particular, a diffraction feature corresponding to a spacing of 8.7 Å has been noted in several studies. Recendy there had been a growing consensus that fcc is the correct structure for sublimed C60. Although the internal carbon atom arrangement of the C60 molecules cannot be determined, the actual packing and defects in C60 crystals over small and relatively large regions are readily seen by HRTEM. We have found by direct imaging a relatively large region of defect-free hep packing of C60 spheres sublimed onto a relatively cool microscopy grid.

scholarly journals Rietveld refinement round robin. I. Analysis of standard X-ray and neutron data for PbSO4

1992 ◽  
Vol 25 (5) ◽  
pp. 589-610 ◽  
Author(s):  
R. J. Hill
Keyword(s):  
Single Crystal ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Data Sets ◽  
X Rays ◽  
Neutron Data ◽  
X Ray ◽  
Atomic Coordinates

The Commission on Powder Diffraction of the International Union of Crystallography has undertaken an intercomparison of Rietveld refinements performed with two `standard' PbSO4 powder diffraction patterns: a conventional (two-wavelength) X-ray pattern collected on a Bragg–Brentano diffractometer with Cu Kα radiation and a constant-wavelength neutron pattern collected on the D1A diffractometer at the Institut Laue–Langevin. The aims of this project were: (i) to evaluate a cross section of currently used Rietveld refinement software; (ii) to examine the range and effect of various strategies of Rietveld refinement; (iii) to assess the precision and accuracy (spread) of the parameters derived by Rietveld analysis. 23 participants provided 18 refinements with the X-ray data and 20 refinements with the neutron data, using 11 different Rietveld-analysis programs. Analysis of the submitted results shows that refinement strategies play a large part in determining the detailed outcome of a Rietveld refinement. The wide variation in the values of the agreement indices obtained in these studies of the same data sets highlights the need for standardization both of the refinement procedures and of the type of data included in the algorithms used for assessing the fit. The major factors limiting the accuracy of the derived PbSO4 crystal structure parameters were: (i) use of insufficiently flexible peak shape and/or background functions; (ii) elimination of the high-angle diffraction data from the refinement; (iii) inclusion of an insufficiently wide range of diffraction angles on either side of the centroid of each peak during the step intensity calculation; and, additionally for X-rays, (iv) simultaneous release of the O-atom site-occupancy and displacement parameters. Rietveld analysis of the PbSO4 X-ray powder diffraction data provided atomic coordinates and isotropic displacement parameters for the Pb and S atoms that are precise (i.e. have small e.s.d.s) and are in reasonable agreement with the values derived from a single crystal study (viz the spread of coordinates is over the range 0.007–0.042 Å). On the other hand, the `light' O-atom parameters show relatively poor precision and have a disconcertingly wide spread of values about the weighted mean (viz 0.12–0.19 Å for the coordinates). Despite the much lower intrinsic resolution of the neutron data (i.e. peak widths some four times those of the X-ray data), the coordinates and anisotropic displacement parameters obtained for the Pb and O atoms are very precise and have a relatively narrow distribution about the single-crystal results, namely 0.004–0.020 Å for the coordinates. The range of coordinates determined from the neutron data for the relatively `light' S atom is correspondingly larger, namely 0.024–0.043 Å, about equivalent to that obtained from the X-ray data. In general, and as expected, the e.s.d.s from the Rietveld analyses are substantially smaller than the observed inter-refinement variation of the unit-cell dimensions, atomic coordinates and isotropic displacement parameters by factors of up to, respectively, 17, 5 and 22 for X-rays, and 25, 3 and 5 for neutrons. This investigation indicates that results of possibly high precision but low accuracy are not uncommon in Rietveld analysis. The disparity between individual refinements can be expected to increase further when, unlike here, the analyses are undertaken using data sets collected under diverse experimental conditions.

Indexing Powder Patterns from Relative Axial Dimensions

1990 ◽  
Vol 5 (2) ◽  
pp. 61-63
Author(s):  
Ben Post ◽  
W. Frank McClune
Keyword(s):  
Data Base ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Single Phase ◽  
Unit Cell ◽  
X Ray ◽  
Large Numbers ◽  
Diffraction Patterns ◽  
Goniometric Measurements ◽  
The One

The usefulness of an X-ray powder diffraction data base, such as the one published by the International Centre for Diffraction Data, is largely dependent on continued additions of indexed powder patterns of single-phase materials of interest to data-base users. The single-phase character of a specimen is generally established by using known values of the unit cell constants to index all its powder pattern lines.In this manuscript we describe indexing procedures based on crystal data which provide only relative values of the cell dimensions, rather than the absolute values usually considered to be essential to the indexing process. To the best of our knowledge, the use of such data for indexing powder diffraction patterns has generally been overlooked or ignored by X-ray crystallographers. We refer to the large numbers of goniometric measurements of crystals which have been published both before, and since, the discovery of X-ray diffraction. These provide useful descriptions of chemical and physical properties of crystals as well as measurements of relative dimensions of unit cell axes. The latter are presented in the form of a/b, b/b and c/b, together with the interaxial angle or angles, if the cell is nonorthogonal.

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