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: Kryptoracemates were found to account for 0.1% of all organic structures containing either a racemic compound, a meso molecule, or some other achiral molecule.
Abstract: A list of 181 organic kryptoracemates has been compiled. This class of crystallographic oddities is made up of racemic compounds (i.e. pairs of resolvable enantiomers) that happen to crystallize in Sohnke space groups (i.e. groups that include only proper symmetry operations). Most (151) of the 181 structures could have crystallized as ordered structures in non-Sohnke groups. The remaining 30 structures do not fully meet this criterion but would have been classified as kryptoracemates by previous authors. Examples were found and checked with the aid of available software for searching the Cambridge Structural Database, for generating and comparing InChI strings, and for validating crystal structures. The pairs of enantiomers in the true kryptoracemates usually have very similar conformations; often the match is near-perfect. There is a pseudosymmetric relationship of the enantiomers in about 60% of the kryptoracemate structures, but the deviations from inversion or glide symmetry are usually quite easy to spot. Kryptoracemates were found to account for 0.1% of all organic structures containing either a racemic compound, a meso molecule, or some other achiral molecule. The centroid of a pair of enantiomers is more likely (99.9% versus 99% probability) to be located on an inversion center than is the centroid of a potentially centrosymmetric molecule.
80 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…Spek, 2009) in batch mode three times: once with default criteria for missed symmetry (angle deviation for any metrical symmetry 1 ; atoms related by inversion or translation 0.45 Å apart; atoms related by other symmetry elements 0.25 Å apart), and then with those tolerances doubled and halved....
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...The structures remaining on the list were again examined usingMercury (Macrae et al., 2008)....
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...Computational tools for that task are available in PLATON (Spek, 2009) andMercury (Macrae et al., 2008)....
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...Molecules are expected to crystallize in low-symmetry space groups (especially P21/c and P1) with asymmetric units that are as small as possible....
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TL;DR: In this article, the evolution of temperature and thermal stresses during friction stir welding of Al6061-T6 was investigated by means of in situ, time resolved neutron diffraction technique.
Abstract: The evolution of temperature and thermal stresses during friction stir welding of Al6061-T6 was investigated by means of in situ, time resolved neutron diffraction technique. A method was developed to deconvolute the temperature and stress from the lattice spacing changes measured by neutron diffraction. The deep penetration capability of neutrons made it possible for the first time to obtain the temperature and thermal stresses inside a friction stir weld.
80 citations
TL;DR: Single crystal X-ray diffraction suggest spin crossover (SCO) and variable temperature magnetic susceptibility measurements confirm thermally driven SCO behaviour in the solid state and in dilute acetone solution centred around 284-288 K.
80 citations
TL;DR: Correcting to the full-spot equivalent, relying on both a physical model for crystal disorder and postrefinement of the crystal orientation, improves the electron density map in serial crystallography.
Abstract: Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shots with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.
79 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...2009), and fully automated fitting of the amino acid sequence was performed with phenix.autobuild (Terwilliger et al., 2008)....
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...In common with previous work on scaling (Hamilton et al., 1965; Fox & Holmes, 1966; Bolotovsky et al., 1998; Kabsch, 2014), here these parameters were determined by iterative non-linear least-squares minimization of a target functional, ¼ X h Ih P rhð ÞG exp 2B sin h 2" # Ih;ref ( )2 ; ð8Þ where h…...
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TL;DR: The energetics of the complex between FMN and the apoflavodoxin from Anabaena PCC 7119 are studied by a combination of site-directed mutagenesis, titration calorimetry, equilibrium binding constant determinations, and x-ray crystallography to understand better the stability of flavoproteins.
79 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