scispace - formally typeset
Search or ask a question
Journal ArticleDOI

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
Journal ArticleDOI
TL;DR: Some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering are highlighted and the progress that has been made is plotted.
Abstract: Studies of diffuse scattering had a prominent place in the first issue of Acta Crystallographica 60 years ago at a time when conventional crystallography (determination of the average structure from Bragg peaks) was in its infancy. Since that time, conventional crystallography has developed enormously while diffuse-scattering analysis has seemingly lagged well behind. The paper highlights some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering and plots the progress that has been made. With the advent of the latest X-ray and neutron sources, area detectors and the ever-increasing power of computers, most disorder problems are now tractable. Two recent contrasting examples are described which highlight what can be achieved by current methods.

39 citations


Cites background from "J. Appl. Cryst.の発刊に際して"

  • ...…have already been used to study a diverse range of problems using diffuse-scattering data, e.g. stacking faults and columnar defects in zeolites (Campbell et al., 2004), defect clustering and local strain in oxide ceramics (Welberry & Christy, 1997), orientational disorder and channel…...

    [...]

Posted Content
TL;DR: The range of sucrose concentration from 30 to 40% created the best experimental conditions for the X-ray small-angle experiment with phospholipid vesicles, and 40% sucrose in H2O increasedX-ray contrast by up to 10 times compared to pure H2 O.
Abstract: The possibility to use sucrose solutions as medium for X-ray and neutron small-angle scattering experiments has been explored for dimyristoylphosphatidylcholine (DMPC) vesicles and mixed DMPC/C_(12)E_(8) aggregates. The influence of sucrose concentration on phospholipid vesicles size and polydispersity has been investigated by complimentary X-ray and neutron scattering. Sucrose solutions decreased vesicle size and polydispersity and increased a contrast between phospholipid membrane and bulk solvent sufficiently for X-rays. 40% sucrose in H2O increased X-ray contrast by up to 10 times compared to pure H2O. The range of sucrose concentration 30%-40% created the best experimental conditions for the X-ray small-angle experiment with phospholipid vesicles.

39 citations


Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...E-mail: kiselev@nf.jinr.ru, fax, 7-096-21-65882; telephone: 7-096-21-66977....

    [...]

  • ...The influence of sucrose concentration on phospholipid vesicles size and polydispersity has been investigated by complimentary X-ray and neutron scattering....

    [...]

  • ...The samples were heated to a temperature above the main phase transition (Tm=23oC) and then cooled down to 10oC....

    [...]

Journal ArticleDOI
TL;DR: In this paper, a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles were reconstructed by using the Poisson-Boltzmann equation to estimate the number of ions bound under different solution conditions.
Abstract: Several algorithms are available to reconstruct low-resolution electron density maps of biological macromolecules from small-angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson–Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson–Boltzmann theory also agree generally well with experimentally determined ion binding numbers.

39 citations


Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...Structures with pairwise NSD values between zero and one are classified as structurally similar....

    [...]

  • ...The NSD has the property that it is zero for identical objects and larger than 1 for objects that systematically differ from one another....

    [...]

  • ...The models resulting from independent runs were superimposed using the SUPCOMB program, which performs an initial alignment of structures based on their axes of inertia followed by minimization of the normalized spatial discrepancy (NSD) (Kozin & Svergun, 2001)....

    [...]

  • ...The Rg values from bead models represent the mean and standard deviation from ten independent reconstructions. hNSDi gives the mean and standard deviations of the pairwise normalized spatial discrepancies between 10 independent reconstructions....

    [...]

  • ...The best superposition of the filtered ‘consensus’ models (see Materials and methods) with the PDB structures was determined using the SUPCOMB (Kozin & Svergun, 2001) program....

    [...]

Journal ArticleDOI
TL;DR: The structure of a recombinant construct consisting of residues 1−245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported in this article.
Abstract: The structure of a recombinant construct consisting of residues 1–245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal α-helix. The structure of the first subdomain (residues 1–117), which consists mostly of β-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.

39 citations

Journal ArticleDOI
01 Aug 2003-EPL
TL;DR: In this paper, the results of neutron powder diffraction studies on the spin-chain compound Ca3CoRhO6 in the temperature range from 3 to 293 K were reported and the most interesting observation was that there is a diffuse magnetic peak superimposed over the strongest magnetic Bragg peak.
Abstract: We report the results of neutron powder diffraction studies on the spin-chain compound Ca3CoRhO6 in the temperature range from 3 to 293 K. Bragg peaks due to magnetic ordering start appearing below about 100 K. The most interesting observation is that there is a diffuse magnetic peak superimposed over the strongest magnetic Bragg peak. The diffuse magnetic intensity is observed below as well as above 100 K. This finding provides a new insight into the physics of this compound as though the low-dimensional magnetic interaction coexists with long-range magnetic order—a novel situation among quasi–one-dimensional oxides.

39 citations

References
More filters
Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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