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: A dynamic view of this flexible molecule was developed by combining the crystal structures with spin-labelling EPR and cross-linking in solution, enabling the first structure determination of a complete DnaJ cochaperone molecule.
Abstract: Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.
30 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...All data were processed with XDS (Kabsch, 1993) or DENZO/ SCALEPACK (Otwinowski & Minor, 1997; Otwinowski, 1993)....
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TL;DR: An analytical method to estimate the thickness of the interface between two phases from small-angle scattering (SAS) data has been developed using Porod's law modified by a triangular smoothing function.
Abstract: An analytical method to estimate the thickness of the interface between two phases from small-angle scattering (SAS) data has been developed using Porod's law modified by a triangular smoothing function. The convolution with a `top-hat' function describing a sharp density profile results in a semi-sigmoidal density profile. This analytical method allows an interfacial layer thickness to be estimated from the negative slope of a Porod plot. The interfacial layer thickness (T) obtained from this model is related to similar models, namely a linear (E) and a sigmoidal density profile (σ) model, as follows: T = 21/2E = 2(61/2)σ, where σ is the standard deviation of the Gaussian function and does not represent the boundary thickness itself. The interfacial layer thickness obtained from any convolution method is a model-dependent parameter.
29 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...On the other hand, Benedetti & Ciccariello (1994) have developed a model for a coated particle assuming three constant electron density regions (not a continuous density pro®le), namely a supporting layer, a void and a coating layer, without relying on a smoothing function.2 The mean scattering…...
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TL;DR: Reaction of the 1-bromoalumole with Mes*Li afforded the corresponding Mes*-substituted alumole (Mes* = 2,4,6-(t-Bu)3C6H2), demonstrating the potential of the1- bromoAlumole for the functionalization of alumoles.
29 citations
TL;DR: The current image makes it possible to discern a single particle covered by a layer of relatively high density that is asymmetrically distributed on the particle surface and shows a partition of high and low densities inside the particle and, in particular, strips of varying density in the lipid core.
Abstract: The knowledge of the molecular structure of LDL, a large lipoprotein complex, is of great interest for medical investigations. Currently available LDL crystals do not diffract to high resolution and do not allow the application of standard crystallographic techniques. Additional difficulties arise because of a very dense crystal packing and the presence of several components with quite different mean densities. Several ab initio phasing methods previously reported by the authors have been successfully applied to find a crystallographic image of LDL at a resolution of 27 A. The most promising results have been obtained using direct phasing with a connectivity analysis of the electron-density maps. The current image makes it possible to discern a single particle covered by a layer of relatively high density that is asymmetrically distributed on the particle surface. It shows a partition of high and low densities inside the particle and, in particular, strips of varying density in the lipid core.
29 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Indexing and integration of the data sets was performed using XDS (Kabsch, 1993)....
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...Values were calculated using the program XSCALE of the XDS package (Kabsch, 1993)....
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...In space groups C222 or C2221 the only possibility for this is to assume that the particle has an internal twofold symmetry and that its centre occupies a special position on a dyad....
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TL;DR: A systematic analysis of diffraction data of 11 different lysozyme crystals (used for cisplatin and carboplatin binding studies) serves as a pilot study for archiving raw diffractionData and associated metadata, which allows for independent assessment of software packages.
Abstract: The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.
29 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...If the reflections are measured in the thinphosphor regime (Chupas et al., 2003), the X-ray absorption is proportional to the path length through the phosphor and intensities should be corrected (Zaleski et al., 1998)....
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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.
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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