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Journal ArticleDOI

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.
Citations
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Journal ArticleDOI
TL;DR: A thorough examination of the disassembly of bimetallic triple-stranded lanthanide helicates in excess of metals shows the competitive formation of standard linearbimetallic complexes and circular trimetallic single-Stranded helicates.

69 citations

Journal ArticleDOI
TL;DR: InteGriTy as discussed by the authors is a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids.
Abstract: InteGriTy is a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids. Tricubic interpolation is used to obtain the density, its gradient and the Hessian matrix at any required position. Critical points and integrated atomic properties have been derived from theoretical densities calculated for the compounds NaCl and TTF-(2,5)Cl(2)BQ (tetrathiafulvalene-2,5-dichlorobenzoquinone), thus covering the different kinds of chemical bonds: ionic, covalent, hydrogen bonds and other intermolecular contacts.

69 citations

Journal ArticleDOI
TL;DR: The crystal structure of coxsackievirus B3 (CVB3) has been determined to 3.5 A resolution and the self-rotation function established pseudo R32 symmetry with each particle sitting on a 32 special position, allowing for a total of six possible monoclinic space-group settings.
Abstract: The crystal structure of coxsackievirus B3 (CVB3) has been determined to 3.5,4, resolution. The icosahedral CVB3 panicles crystallize in the monoclinic space group, P21, (a-- 574.6, b = 302.1, c--- 521.6A, /3--107.7 °) with two virions in the asymmetric unit giving 120-fold non-crystallographic redundancy. The crystals diffracted to 2.7 A resolution and the X-ray data set was 55% complete to 3.0,4, resolution. Systematically weak reflections and the self-rotation function established pseudo R32 symmetry with each particle sitting on a 32 special position. This constrained the orientation and position of each panicle in the monoclinic cell to near face-centered positions and allowed for a total of six possible monoclinic spacegroup settings. Correct interpretation of the highresolution (3.0-3.2~,) self-rotation function was instrumental in determining the deviations from R32 orientations of the virus particles in the unit cell. Accurate particle orientations permitted the correct assignment of the crystal space-group setting amongst the six ambiguous possibilities and for the correct determination of particle positions. Real-space electron-density averaging and phase refinement, using human rhinovius 14 (HRV14) as an initial phasing model, have been carried out to 3.5,~ resolution. The initial structural model has been built and refined to 3.5 ~, resolution using X-PLOR.

69 citations

Journal ArticleDOI
TL;DR: This review attempts to provide a comprehensive introduction to major computer programs, especially on-line servers, for protein modeling by addressing what a user can expect from the computer tools in terms of their strengths and limitations.
Abstract: Protein modeling is playing a more and more important role in protein and peptide sciences due to improvements in modeling methods, advances in computer technology, and the huge amount of biological data becoming available. Modeling tools can often predict the structure and shed some light on the function and its underlying mechanism. They can also provide insight to design experiments and suggest possible leads for drug design. This review attempts to provide a comprehensive introduction to major computer programs, especially on-line servers, for protein modeling. The review covers the following aspects: (1) protein sequence comparison, including sequence alignment/search, sequence-based protein family classification, domain parsing, and phylogenetic classification; (2) sequence annotation, including annotation/prediction of hydrophobic profiles, transmembrane regions, active sites, signaling sites, and secondary structures; (3) protein structure analysis, including visualization, geometry analysis, structure comparison/classification, dynamics, and electrostatics; (4) three-dimensional structure prediction, including homology modeling, fold recognition using threading, ab initio prediction, and docking. We will address what a user can expect from the computer tools in terms of their strengths and limitations. We will also discuss the major challenges and the future trends in the field. A collection of the links of tools can be found at http://compbio.ornl.gov/structure/resource/.

69 citations

Journal ArticleDOI
TL;DR: This species performs four electron cleavage of azobenzene to generate the uranium bis(imido), Cp*(PDI)U(NPh)2, which features a triply reduced PDI ligand.

68 citations

References
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Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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