J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: Binary complexes of the human deletion mutant, DeltaG6PD, with glucose-6-phosphate and NADP(+) have been crystallized and their structures solved to 2.9 and 2.5 A, respectively, suggesting flexibility in the predominantly hydrophilic dimer-dimer interactions.
Abstract: Human glucose-6-phosphate dehydrogenase (G6PD) is NADP+-dependent and catalyses the first and rate-limiting step of the pentose phosphate shunt. Binary complexes of the human deletion mutant, ΔG6PD, with glucose-6-phosphate and NADP+ have been crystallized and their structures solved to 2.9 and 2.5 A, respectively. The structures are compared with the previously determined structure of the Canton variant of human G6PD (G6PDCanton) in which NADP+ is bound at the structural site. Substrate binding in ΔG6PD is shown to be very similar to that described previously in Leuconostoc mesenteroides G6PD. NADP+ binding at the coenzyme site is seen to be comparable to NADP+ binding in L. mesenteroides G6PD, although some differences arise as a result of sequence changes. The tetramer interface varies slightly among the human G6PD complexes, suggesting flexibility in the predominantly hydrophilic dimer–dimer interactions. In both complexes, Pro172 of the conserved peptide EKPxG is in the cis conformation; it is seen to be crucial for close approach of the substrate and coenzyme during the enzymatic reaction. Structural NADP+ binds in a very similar way in the ΔG6PD–NADP+ complex and in G6PDCanton, while in the substrate complex the structural NADP+ has low occupancy and the C-terminal tail at the structural NADP+ site is disordered. The implications of possible interaction between the structural NADP+ and G6P are considered.
138 citations
TL;DR: The foundations and current features of a widely used graphical user interface for macromolecular crystallography are described.
Abstract: A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.
137 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Most of the current generation of graphical interfaces have focused on making the individual steps as accessible as possible and linking them together, rather than imposing ‘black-box’ automation on the user (Potterton et al., 2003; Pape & Schneider, 2004; Minor et al., 2006; Emsley et al., 2010)....
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...The resulting package is easily maintained and extended as new programs are added or modified....
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15 Dec 2004-Materials Science and Engineering A-structural Materials Properties Microstructure and Processing
TL;DR: In this article, the effect of Mg addition on the microstructural evolution and mechanical properties of high-purity aluminum was studied over a wide range of strain, up to ∼8.
Abstract: The effect of Mg addition on the microstructural evolution and mechanical properties of high-purity aluminum was studied over a wide range of strain, up to ∼8. The high strains were achieved by applying the equal-channel angular pressing technique. The stress–strain relationship was related to the evolution of the microstructure investigated by transmission electron microscopy and X-ray diffraction peak profile analysis. In the early stages of plastic deformation the interaction between the dislocations and the Mg solute atoms results in an increase of the flow stress with temperature. The stable microstructure is developed at higher strains owing to the Mg addition resulting in the saturation of the proof stress at higher strains in Al–Mg alloys.
136 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...E-mail address:gubicza@ludens.elte.hu (J. Gubicza). and Al–Mg alloys are compared after compression testing and ECAP deformation....
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TL;DR: In this paper, the size-broadened profile given by the lognormal and gamma size distributions of spherical crystallites is considered and an analytical approximation is derived that can be analytically convolved with the strain broadened and instrumental broadened profiles.
Abstract: The size-broadened profile given by the lognormal and gamma size distributions of spherical crystallites is considered. An analytical approximation for the size-broadened profile is derived that can be analytically convolved with the strain-broadened and instrumental-broadened profiles. The method is tested on two CeO2 powders; one shows `super-Lorentzian' profiles that were successfully modelled under the assumption of a broad lognormal size distribution. It is shown that the Voigt function, as a common model for a size-broadened profile, fails for both very narrow and broad size distributions. It is argued that the size-broadened line profile is not very sensitive to variations in size distribution and that an apparent domain size or even column-length distribution function can correspond to significantly different size distributions.
134 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...It is argued that the sizebroadened line pro®le is not very sensitive to variations in size distribution and that an apparent domain size or even column-length distribution function can correspond to signi®cantly different size distributions....
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...It was found (Balzar & Ledbetter, 1993) that the size-broadened Voigt function requires the ratio of volume-averaged and area-averaged domains to be in the range [1.31, 2) in order for the column-length distribution function to be positive....
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...Especially, it has been shown that modeling both size-broadened and strain-broadened pro®les by Voigt functions (Langford, 1980; Balzar & Ledbetter, 1993) is much more ¯exible and able to accommodate different sample types and deformations....
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TL;DR: The distribution of anisotropy within each of these refined models is broadly similar across the entire set of structures, with a significant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and Rfree.
Abstract: Recent technological improvements in crystallographic data collection have led to a surge in the number of protein structures being determined at atomic or near-atomic resolution. At this resolution, structural models can be expanded to include anisotropic displacement parameters (ADPs) for individual atoms. New protocols and new tools are needed to refine, analyze and validate such models optimally. One such tool, PARVATI, has been used to examine all protein structures (peptide chains >50 residues) for which expanded models including ADPs are available from the Protein Data Bank. The distribution of anisotropy within each of these refined models is broadly similar across the entire set of structures, with a mean anisotropy A in the range 0.4–0.5. This is a significant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and Rfree. The observed distribution of anisotropy may prove useful in the validation of very high resolution structures. A more complete understanding of this distribution may also allow the development of improved protein structural models, even at lower resolution.
134 citations
References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
18,531 citations
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations