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: In this article, a cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass, and simulations are performed at different hydration levels.
Abstract: We present results of molecular dynamics simulations of water confined in a silica pore. A cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass. The simulations are performed at different hydration levels. At all hydration levels water adsorbs strongly on the Vycor surface; a double layer structure is evident at higher hydrations. At almost full hydration the modifications of the confinement-induced site-site pair distribution functions are in qualitative agreement with neutron diffraction experiment. A decrease in the number of hydrogen bonds between water molecules is observed along the pore radius, due to the tendency of the molecules close to the substrate to form hydrogen-bonds with the hydrophilic pore surface. As a consequence we observe a substrate induced distortion of the H-bond tetrahedral network of water molecules in the regions close to the surface.
67 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...In addition both BO’s and NBO’s interact C. Hartnig et al., Figure 1 with the oxygen sites of water via a Lennard-Jones potential, whose parameters areσ = 2.70 Å and σ = 3.00 Å for BO and NBO atoms, respectively, andε = 230 K in both cases [11]....
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TL;DR: A computationally efficient method is presented - 'fast rotational matching' or FRM - that significantly accelerates the search of the three rotational degrees of freedom (DOF) in biomolecular matching problems.
Abstract: A computationally efficient method is presented – `fast rotational matching' or FRM – that significantly accelerates the search of the three rotational degrees of freedom (DOF) in biomolecular matching problems. This method uses a suitable parametrization of the three-dimensional rotation group along with spherical harmonics, which allows efficient computation of the Fourier Transform of the rotational correlation function. Previous methods have used Fourier techniques only for two of the rotational DOFs, leaving the remaining angle to be determined by an exhaustive search. Here for the first time a formulation is presented that makes it possible to Fourier transform all three rotational DOFs, resulting in notable improvements in speed. Applications to the docking of atomic structures into electron-microscopy maps and the molecular-replacement problem in X-ray crystallography are considered.
67 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...We have made a timing comparison between our approach and a `Crowther-like' modi®cation of it in which the computation of the dlmm0 is performed on the ¯y (Crowther, 1972), as is the case in packages such as AMoRe (Navaza, 1994) and MOLREP (Vagin & Teplyakov, 1997)....
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...D58, 1282±1286 Kovacs & Wriggers Fast rotational matching 1283 1 This convention is the same as that used by Crowther (1972) and in programs in the CCP4 suite such as AMoRe (Navaza, 1994) and MOLREP (Vagin & Teplyakov, 1997)....
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TL;DR: This system uses simple hardware, leaves the substrate unaltered, and shows that SABRE is potentially suitable for clinical purposes.
Abstract: NMR signal amplification by reversible exchange (SABRE) has been observed for pyridine, methyl nicotinate, N-methylnicotinamide, and nicotinamide in D2 O with the new catalyst [Ir(Cl)(IDEG)(COD)] (IDEG=1,3-bis(3,4,5-tris(diethyleneglycol)benzyl)imidazole-2-ylidene) During the activation and hyperpolarization steps, exclusively D2 O was used, resulting in the first fully biocompatible SABRE system Hyperpolarized (1) H substrate signals were observed at 425 MHz upon pressurizing the solution with parahydrogen at close to the Earth's magnetic field, at concentrations yielding barely detectable thermal signals Moreover, 42-, 26-, 22-, and 9-fold enhancements were observed for nicotinamide, pyridine, methyl nicotinate, and N-methylnicotinamide, respectively, in conventional 300 MHz studies This research opens up new opportunities in a field in which SABRE has hitherto primarily been conducted in CD3 OD This system uses simple hardware, leaves the substrate unaltered, and shows that SABRE is potentially suitable for clinical purposes
67 citations
TL;DR: Simple formulae are developed in this paper to explain capillary performance given the X-ray source size, capillary dimensions and slope errors, and capillary length is optimized for best focusing performance.
Abstract: Single-bounce hollow glass capillaries with ellipsoidal shapes have been used at the Cornell High Energy Synchrotron Source recently for various microbeam experiments, with focal spot sizes from 12 to 23 µm, divergences from 2 to 8 mrad, intensities up to 450 times the intensities of incident X-rays, and working distances up to 55 mm. Simple formulae are developed in this paper to explain capillary performance given the X-ray source size, capillary dimensions and slope errors. Capillary length is optimized for best focusing performance. Capillary fabrication accuracy is reported and capillary X-ray tests confirm the focusing properties expected from formulae. The application of capillaries to third-generation X-ray sources and future energy-recovery linac X-ray sources are discussed.
67 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...…working distance, controlled maximum beam divergence, higher X-ray throughput, and more likely a lower background because the total reflection from a SBC prevents X-rays from penetrating the glass wall material as they may in the multibounce case (Engström & Riekel, 1996b; Riekel et al., 2000)....
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TL;DR: The crystal structure of the ligand binding domain of the γ isotype of human PPAR in complex with ajulemic acid shows a binding mode that is compatible with other known partial agonists of PPAR, explaining their moderate activation of the receptor, and provides clues to the understanding of partial agonism itself.
67 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