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: The growth processes and defect structures of protein and virus crystals have been studied in situ by atomic force microscopy, X-ray diffraction topography, and high-resolution reciprocal space scanning, finding fundamental insights into the improvement of macromolecular crystallization protocols are discussed.
51 citations
TL;DR: Systematic SAXS simulations have been analysed over a wide range of parameters in order to better understand the detergent corona around a membrane protein.
Abstract: The application of small-angle X-ray scattering (SAXS) to structural investigations of transmembrane proteins in detergent solution has been hampered by two main inherent hurdles. On the one hand, the formation of a detergent corona around the hydrophobic region of the protein strongly modifies the scattering curve of the protein. On the other hand, free micelles of detergent without a precisely known concentration coexist with the protein–detergent complex in solution, therefore adding an uncontrolled signal. To gain robust structural information on such systems from SAXS data, in previous work, advantage was taken of the online combination of size-exclusion chromatography (SEC) and SAXS, and the detergent corona around aquaporin-0, a membrane protein of known structure, could be modelled. A precise geometrical model of the corona, shaped as an elliptical torus, was determined. Here, in order to better understand the correlations between the corona model parameters and to discuss the uniqueness of the model, this work was revisited by analyzing systematic SAXS simulations over a wide range of parameters of the torus.
51 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...In order to ensure accuracy in the final results and also the fastest possible run time, the user is asked to limit the number of spherical harmonics L used by CRYSOL according to the relation L = 5 + QmaxDmax/2, where Qmax is the maximum considered momentum transfer and Dmax is the maximum diameter of the protein–detergent complex that may be estimated from the experimental data using GNOM (Svergun, 1992)....
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...…the number of spherical harmonics L used by CRYSOL according to the relation L = 5 + QmaxDmax/2, where Qmax is the maximum considered momentum transfer and Dmax is the maximum diameter of the protein–detergent complex that may be estimated from the experimental data using GNOM (Svergun, 1992)....
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TL;DR: In this article, electron backscatter diffraction (EBSD) was used to investigate the growth of gold bonding wires. But the results were limited to a single wire drawn to an equivalent strain greater than 11.4 with final diameter between 25 and 30 µm.
Abstract: Recrystallization and grain growth of gold bonding wire have been investigated with electron back-scatter diffraction (EBSD). The bonding wires were wire-drawn to an equivalent strain greater than 11.4 with final diameter between 25 and 30 µm. Annealing treatments were carried out in a salt bath at 300 °C, and 400 °C for 1, 10, 60 minutes, and 1 day. The textures of the drawn gold wires contain major 〈111〉, minor 〈100〉, and small fractions of complex fiber components. The 〈100〉 oriented regions are located in the center and surface of the wire, and the complex fiber components are located near the surface. The 〈111〉 oriented regions occur throughout the wire. Maps of the local Taylor factor can be used to distinguish the 〈111〉 and 〈100〉 regions. The 〈111〉 oriented grains have large Taylor factors and might be expected to have higher stored energy as a result of plastic deformation compared to the 〈100〉 regions. Both 〈111〉 and 〈100〉 grains grow during annealing. In particular, 〈100〉 grains in the surface and the center part grow into the 〈111〉 regions at 300 °C and 400 °C. Large misorientations (angles >40 deg) are present between the 〈111〉 and 〈100〉 regions, which means that the boundaries between them are likely to have high mobility. Grain average misorientation (GAM) is greater in the 〈111〉 than in the 〈100〉 regions. It appears that the stored energy, as indicated by geometrically necessary dislocation content in the subgrain structure, is larger in the 〈111〉 than in the 〈100〉 regions.
51 citations
TL;DR: A new monoclinic polymorph, form II, of 3,4-dimethoxycinnamic acid has been isolated and shows a different photochemical and photomechanical property from the previously reported triclinic form I.
51 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The structure solution was performed by direct methods, and refinements were executed using SHELX97 (Sheldrick, 2008) and the WinGX (Farrugia, 1999) suite of programs....
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TL;DR: The crystal structure of hexagonal L-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa.
Abstract: The crystal structure of hexagonal l-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa. The structure of this phase consists of molecules in their zwitterionic form, and crystallizes in the hexagonal space group P6122. The structure consists of hydrogen-bonded layers which are strongly reminiscent of those seen in α-glycine, and consist of R_4^4(16) hydrogen-bonded ring motifs. These layers are connected on one side by the disulfide bridges within the cystine molecules, and on the other by NH⋯O hydrogen bonds to other glycine-like layers. The most compressible unit-cell dimension, and the direction of greatest strain in the structure, is along the c-axis, and application of pressure pushes the layers closer together. The compression occurs approximately equally in the regions of the interlayer hydrogen bonds and the disulfide bridges; in the latter, changes in the C—S—S—C torsion angles allow the cystine molecules to act like springs. The effects of pressure can be interpreted in terms of closing-up of voids in the structure, and this leads to (i) a lessening of the N—C—C—O and C—S—S—C torsional angles, (ii) shortening of the N—H⋯O hydrogen bonds by 0.10–0.60 A and (iii) a further shortening of an already short S⋯S contact from 3.444 (4) A to 3.264 (4) A.
51 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