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
More filters
TL;DR: An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained after extensive crystallization trials and various novel crystal structure analyses.
Abstract: Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.
34 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The crystal structures were solved using molecular replacement with Phaser (McCoy et al., 2007), using the reported lysozyme structure with PDB code 2w1y as a molecular search model (Cianci et al., 2008) and restrained refinement with REFMAC5 (Murshudov et al., 2011) from CCP4 (Winn et al., 2011)....
[...]
TL;DR: In this paper, the authors used the Sim distribution and the Cochran distribution to identify phase doublets from SAD data prior to density modification, and the results showed that using direct-methods phases based on the product of the Sim and Cochran distributions can lead to improved initial phases.
Abstract: In the initial stage of SAD phasing, the essential point is to break the intrinsic phase ambiguity The presence of two kinds of phase information enables the discrimination of phase doublets from SAD data prior to density modification One is from the heavy atoms (anomalous scatterers), while the other is from the direct-methods phase relationships The former can be expressed by the Sim distribution, while the latter can be expressed by the Cochran distribution Typically, only the Sim distribution has been used to yield initial phases for subsequent density modification However, it has been demonstrated that using direct-methods phases based on the product of the Sim and Cochran distributions can lead to improved initial phases In this paper, the direct-methods phasing procedure OASIS has been improved and combined with the SOLVE/RESOLVE procedure Experimental SAD data from three known proteins with expected Bijvoet ratios 〈|ΔF|〉/〈F〉 in the range 14–70% were used as test cases In all cases, the phases obtained using the program RESOLVE beginning with initial phases based on experimental phases plus Sim and direct-methods information were more accurate than those based on experimental plus Sim phase information alone
34 citations
TL;DR: Imaging with surface- and bulk-sensitive electron and X-ray diffraction based microscopic techniques enabled identification of the twin domain distribution of Bi2Te3 and Bi2Se3 thin films.
Abstract: The twin distribution in topological insulators Bi2Te3 and Bi2Se3 was imaged by electron backscatter diffraction (EBSD) and scanning X-ray diffraction microscopy (SXRM). The crystal orientation at the surface, determined by EBSD, is correlated with the surface topography, which shows triangular pyramidal features with edges oriented in two different orientations rotated in the surface plane by 60°. The bulk crystal orientation is mapped out using SXRM by measuring the diffracted X-ray intensity of an asymmetric Bragg peak using a nano-focused X-ray beam scanned over the sample. By comparing bulk- and surface-sensitive measurements of the same area, buried twin domains not visible on the surface are identified. The lateral twin domain size is found to increase with the film thickness.
34 citations
TL;DR: In this paper, a method is developed for constructing the stress orientation distribution function from strain pole figures measured with a pulsed neutron source and demonstrated with cold-rolled interstitial-free steel.
Abstract: The stress orientation distribution function (SODF) was recently introduced as a mean-field representation to describe the grain-orientation dependence of intergranular stress Pulsed neutron sources are ideally suited for the determination of the SODF since multiple reflections can be measured simultaneously with comparable precision A method is developed for constructing the SODF from strain pole figures measured with a pulsed neutron source and demonstrated with cold-rolled interstitial-free steel The experimental results are compared with those measured with a reactor-based constant-wavelength diffractometer It is shown that access to a large number of reflections on a pulsed neutron source improves the precision of the experimental SODF and facilitates in situ studies of the evolution of the intergranular stress during deformation and annealing
34 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Popa & Balzar (2001) have recently explored this possibility....
[...]
TL;DR: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves a community of users with diverse backgrounds and interests and develops educational resources and materials to enable people to utilize PDB data and to further a structural view of biology.
Abstract: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.
34 citations
References
More filters
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