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 high-resolution scattering length density analysis method has been generalized from unilamellar to multilameLLar lipid vesicles, yielding an improved refinement of the lipid backbone position.
Abstract: The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.
65 citations
Additional excerpts
...Two-dimensional data were reduced using MantidPlot (http://www.mantidproject.org/)....
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TL;DR: Hybrid and monolithic detectors for X-ray imaging are reviewed and new approaches are proposed for using nanofiltration and x-ray diffraction techniques to improve the quality of these detectors.
65 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...We then present selected on-going MAPS and related projects....
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TL;DR: The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common as mentioned in this paper, which can 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.
Abstract: 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.
65 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Modifications to the program TLSANL and to the CCP4i interface have been contributed to the CCP4 project....
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...Segmented TLS entries refined with REFMAC that did not already contain individual ANISOU records for the protein or DNA atoms were run through TLSANL (Howlin et al., 1993) to generate them from the TLS model....
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...Entries refined by either REFMAC or PHENIX that already included ANISOU records were analyzed without running TLSANL (350 entries)....
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...The program TLSANL (Howlin et al., 1993) has been extended to calculate the residuals ccuij, rSIMU and rDELU for each C—...
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...Anisotropy and correlation of anisotropy were analyzed for the entries successfully processed by TLSANL (2642 entries)....
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TL;DR: In this article, a modified Williamson-Hall and modified Warren-Averbach methods are proposed to yield physically well justified data for particle size, dislocation densities and twinning and faulting.
Abstract: Numerous experiments have shown that strain broadening caused by dislocations can be well described by a special logarithmic series expansion of the Fourier coefficients of Bragg reflection peak profiles. In the present work it will be shown that this formalism can be incorporated into the classical methods of Williamson-Hall and Warren-Averbach. The new procedures are suggested to be called modified Williamson-Hall and modified WarrenAverbach methods, respectively. Based on the examples of a submicron grain size copper specimen and a ball-milled iron powder sample it is going to be shown that the modzjied methods can yield physically well justified data for particle size, dislocation densities and twinning and faulting.
65 citations
Journal Article•
TL;DR: The structure of Pseudomonas fluorescens carboxyl esterase (PFE) was solved to a resolution of 1.8ÅA by X-ray diffraction as mentioned in this paper.
64 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