Rapid model building of β-sheets in electron-density maps
- Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
A method for rapid model building of β-sheets at moderate resolution is presented. A method for rapidly building β-sheets into electron-density maps is presented. β-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C{sup β} atoms along the strand averaged over all repeats present in the strand. The β-strands obtained are then assembled into a single atomic model of the β-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. The β-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 Å resolution in which a third of the residues in β-sheets were built and a structure at 3.8 Å in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 Å.
- OSTI ID:
- 22347929
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 66, Issue Pt 3; Other Information: PMCID: PMC2827348; PMID: 20179339; PUBLISHER-ID: dz5183; OAI: oai:pubmedcentral.nih.gov:2827348; Copyright (c) Terwilliger 2010; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
Rapid chain tracing of polypeptide backbones in electron-density maps
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journal | February 2010 |
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