issue contents

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047

August 2006 issue

Get-Phases 2005

Highlighted illustration

Cover illustration: This figure illustrates the packing of the small-angle X-ray scattering (SAXS) envelope in the crystallographic unit cell of nitrite reductase. The molecular replacement solution was found with the FSEARCH program (p. 909).



research papers


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A large-scale, cost-effective, semi-automated platform for structural genomics has been set up at Peking University and this platform is aiming at a cost of US $10 000 per structure determination.

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Beamline automation has significantly improved the throughput and accuracy of X-ray data collection from biological molecules. Further improvements will make the systems even more robust and offer a route to optimized and remote data collection.

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An expert system for semi-automatic or automatic analysis of X-ray diffraction data has been developed and used for over 140 new structure determinations. The typical end result is an interpretable electron-density map with a partially built structure.

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Various criteria used for estimation of the anomalous signal in diffraction data are discussed.

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A database is presented of heavy-atom derivatives that have been used in structure determination of membrane proteins. Compounds of organo-mercurials, PtII and trimethyl-lead are particularly successful.

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Iterative dual-space fragment extension with protein SAD data is performed by a combination of the programs OASIS-2004, DM, RESOLVE (build only) and ARP/wARP. The procedure is beneficial to high-throughput protein structure determination.

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Examples of Cr SAD structure solutions using a Cr/Cu dual-wavelength system in combination with a loopless free crystal-mounting method are shown.

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Recent development on statistical direct phasing methods for heavy-atom substructure determination has been outlined.

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ACORN has been used to solve a number of protein structures and has been extended to work with data to resolution down to 1.7 Å.

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This paper describes the development of the FSEARCH program for locating envelopes in the unit cell and possible ways to extend phases to crystallographic data resolution.

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An automated ligand-fitting procedure has been developed and tested on 9327 ligands and (FoFc)exp(iφc) difference density from macromolecular structures in the Protein Data Bank.

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Methods and considerations for the structure solution and refinement of the ATPase p97/VCP at 4.7 to 3.5 Å resolution are described.

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The crystal structures of bacterial ribonuclease III (RNase III) in complex with double-stranded (ds) RNA provide a structural basis for its non-catalytic and catalytic activities and insight into the mechanism of dsRNA processing by all members of the RNase III family.

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The analysis of the translation apparatus has made it eminently clear that the complementarity of structural methods is needed to get an understandable and reasonably clear picture.
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