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 structure of the network forming glass GeO(2) is investigated by making the first application of the method of in situ neutron diffraction with isotope substitution at pressures increasing from ambient to 8 GPa, with results in quantitative agreement only with molecular dynamics simulations made using interaction potentials that include dipole-polarization effects.
Abstract: The structure of the network forming glass GeO2 is investigated by making the first application of the method of in situ neutron diffraction with isotope substitution at pressures increasing from ambient to 8 GPa. Of the various models, the experimental results are in quantitative agreement only with molecular dynamics simulations made using interaction potentials that include dipole-polarization effects. When the reduced density ρ/ρ0 ≳ 1.16, where ρ0 is the value at ambient pressure, network collapse proceeds via an interplay between the predominance of distorted square pyramidal GeO5 units versus octahedral GeO6 units as they replace tetrahedral GeO4 units. This replacement necessitates the formation of threefold coordinated oxygen atoms and leads to an increase with density in the number of small rings, where a preference is shown for sixfold rings when ρ/ρ0 = 1 and fourfold rings when ρ/ρ0 = 1.64.
40 citations
TL;DR: Mo Kα1 patterns were found to yield slightly more accurate analyses than those derived from Cu’s radiation, and the quantifications have been carried out by using calibration curves with increasing amounts of a given phase.
Abstract: This study reports 78 Rietveld quantitative phase analyses using Cu Kα1, Mo Kα1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo Kα1 radiation have slightly better accuracies than those obtained from Cu Kα1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback–Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%.
40 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...From the (slight) overestimation of the standard, the amorphous content of the investigated sample is derived (De la Torre et al., 2001)....
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...The absorption factor of each sample was experimentally measured by comparing the direct beam with and without the sample (Cuesta et al., 2015)....
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...The overall amorphous content was determined from the internal standard methodology approach (De la Torre et al., 2001; Aranda et al., 2012)....
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TL;DR: The first atropisomeric phosphinine was designed and prepared by introducing substituents into specific positions of the heterocyclic framework; the presence of axial chirality was predicted and experimentally verified by chiral HPLC analysis, derivatization experiments as well as temperature dependent 31P{1H} NMR spectroscopy.
Abstract: The first atropisomeric phosphinine was designed and prepared by introducing substituents into specific positions of the heterocyclic framework; the presence of axial chirality was predicted by means of DFT calculations and experimentally verified by chiral HPLC analysis, derivatization experiments as well as temperature dependent 31P{1H} NMR spectroscopy.
40 citations
TL;DR: The X-ray structure of hen egg-white lysozyme co-crystallized in the presence of alcohols with varying hydrophobicities has been studied and it is believed that the disorder induced in the water molecules is a direct consequence of alcohol binding.
Abstract: Organic solvents are known to bring about dehydration of proteins, the molecular basis of which has remained uncharacterized. The dehydration effect in many cases leads to eventual unfolding of proteins through the macroscopic solvent effect. In some cases, the organic solvent molecules also bind to protein surfaces, thereby forcing local unfolding. The X-ray structure of hen egg-white lysozyme co-crystallized in the presence of alcohols with varying hydrophobicities has been studied. It was noticed that although the alcohols have very little effect on the conformation of the overall protein structure, they profoundly affect protein hydration and disorder of the bound waters. Systematic analysis of the water structure around the lysozyme molecule suggests that an increasing order of hydrophobicity of alcohols is directly proportional to the higher number of weakly bound waters in the protein. As anticipated, the water molecules in the native structure with high temperature factors (>/=40 A(2)) attain higher disorder in the presence of alcohols. It is believed that the disorder induced in the water molecules is a direct consequence of alcohol binding.
40 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The quality of the refined structure was determined using PROCHECK (Laskowski et al., 1993)....
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TL;DR: The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity.
Abstract: The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 A was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily α-β-β-α fold. Association in the hexamer preserves the eight-layered α-β-β-α:α-β-β-α structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity.
40 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The accuracy, precision and correctness of the refined G. pallidus RAPc8 amidase model was assessed using various validation tools, including PROCHECK (Collaborative Computational Project, Number 4, 1994; Laskowski et al., 1993), WHATCHECK (Hooft et al., 1996) and MOLPROBITY (Lovell et al., 2003)....
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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.
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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.
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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'.
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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.
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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