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 sulfur SAD phasing method was successfully used to determine the structure of the N-terminal domain of HCV E1 from low-resolution diffracting crystals by combining data from 32 crystals.
Abstract: Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 A resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 A resolution model building was achievable.
33 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The sulfur substructure was determined using the HKL2MAP graphical interface (Pape & Schneider, 2004) with SHELXC, SHELXD and SHELXE (Sheldrick, 2010)....
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...SAD phasing was performed by phenix.autosol (Adams et al., 2002) using the sulfur sites obtained by HKL2MAP (Pape & Schneider, 2004)....
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...D70, 2197–2203 Figure 2 HKL2MAP profiles....
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TL;DR: There can be an experimentally detectable influence of ions on binary liquid mixtures due to steric effects but not due to charge effects, and the bilinear coupling approximation is compared with a novel local density approximation for the ion-solvent interactions.
Abstract: The influence of ions on the bulk phase behavior of binary liquid mixtures acting as their solvents and on the corresponding interfacial structures close to a planar wall is investigated by means of density functional theory based on local descriptions of the effective interactions between ions and their solvents. The bilinear coupling approximation (BCA), which has been used in numerous previous related investigations, is compared with a novel local density approximation (LDA) for the ion-solvent interactions. It turns out that within BCA the bulk phase diagrams, the two-point correlation functions, and critical adsorption exhibit qualitative features which are not compatible with the available experimental data. These discrepancies do not occur within the proposed LDA. Further experimental investigations are suggested which assess the reliability of the proposed LDA. This approach allows one to obtain a consistent and rather general understanding of the effects of ions on solvent properties. From our analysis we infer in particular that there can be an experimentally detectable influence of ions on binary liquid mixtures due to steric effects but not due to charge effects.
33 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Within Ginzburg-Landau theory the extrapolation length z0 is fixed by the boundary condition φ ′(0) = −3h/χ....
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...I. INTRODUCTION Ion-solvent mixtures play a central role for various important soft matter systems such as colloidal suspensions, polymer solutions, biochemical reactions, and electrochemical cells....
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TL;DR: The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.
Abstract: Hepatitis B core (HBc) particles have been extensively exploited as carriers for foreign immunological epitopes in the development of multicomponent vaccines and diagnostic reagents. Crystals of the T = 4 HBc particle were grown in PEG 20 000, ammonium sulfate and various types of alcohols. A temperature jump from 277 or 283 to 290 K was found to enhance crystal growth. A crystal grown using MPD as a cryoprotectant diffracted X-rays to 7.7 A resolution and data were collected to 99.6% completeness at 8.9 A. The crystal belongs to space group P212121, with unit-cell parameters a = 352.3, b = 465.5, c = 645.0 A. The electron-density map reveals a protrusion that is consistent with the N-terminus extending out from the surface of the capsid. The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.
33 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...A self-rotation function was performed using the program MOLREP (Vagin & Teplyakov, 1997)....
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TL;DR: The structure of the single-stranded DNA phage phiX174 has been determined to 3.4 A resolution and the resultant electron density map was readily interpreted in terms of the F, G and J polypeptides in the capsid.
Abstract: The structure of the single-stranded DNA phage phiX174 has been determined to 3.4 A resolution. The crystal space group was P2(1) with one icosahedral particle per asymmetric unit, giving 60-fold noncrystallographic redundancy. Oscillation diffraction photographs were collected using synchrotron radiation at various wavelengths. The particle orientations in the unit cell were determined with a rotation function. Because cowpea mosaic virus has a similar external envelope to phiX174, it was used as a search model to find the approximately positions of the phiX174 particles in the unit cell relative to the crystallographic symmetry axes. An initial phase set to 12 A resolution was then based on the cowpea mosaic virus atomic structure. These phases were improved by 20 cycles of real-space molecular replacement averaging. The phase information was gradually extended to 3.4 A resolution by molecular replacement electron density averaging. One reciprocal lattice point was used for each extension followed by four cycles of averaging. The unusual particle capsid, with its 12 pentameric spikes, required the careful determination of a precise molecular envelope. This was redetermined at regular intervals, as was the particle center. The resultant electron density map was readily interpreted in terms of the F, G and J polypeptides in the capsid. A difference electron density map between full and partially empty particles showed some ordered DNA structure.
33 citations
Additional excerpts
...These were then processed (Rossmann, 1979) ,...
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01 Sep 2001-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: The region of sucrose concentrations 30–40% created the best experimental conditions for X-ray small-angle experiments with phospholipid vesicles, and no influence of Sucrose on the membrane thickness or mutual packing of hydrocarbon chains has been detected.
Abstract: The small-angle X-ray and neutron scattering, time resolved X-ray small-angle and wide-angle diffraction coupled with differential scanning calorimetry have been applied to the investigation of unilamellar and multilamellar dimyristoylphosphatidylcholine vesicles in sucrose buffers with sucrose concentrations from 0% to 60%. Sucrose buffer decreased vesicle size and polydispersity and increased an X-ray contrast between phospholipid membrane and bulk solvent sufficiently. No influence of sucrose on the membrane thickness or mutual packing of hydrocarbon chains has been detected. The region of sucrose concentrations 30–40% created the best experimental conditions for X-ray small-angle experiments with phospholipid vesicles.
33 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Nuclear Instruments & Methods in Physics Research A 470 (2001) 409-416...
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...D, B.P. 34, F-91898 Orsay, France % - Pharmaceutical Faculty, University Paris-Sud, Chatenay Malabry F – 92296, France...
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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'.
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