skip to main content

SciTech ConnectSciTech Connect

Title: Model morphing and sequence assignment after molecular replacement

A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. Themore » procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [3] ;  [1]
  1. Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States)
  2. University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY (United Kingdom)
  3. Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States)
  4. Stanford University, 318 Campus Drive West, Stanford, CA 94305 (United States)
Publication Date:
OSTI Identifier:
22347837
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 69; Journal Issue: Pt 11; Other Information: PMCID: PMC3817698; PMID: 24189236; PUBLISHER-ID: ba5205; OAI: oai:pubmedcentral.nih.gov:3817698; Copyright (c) Terwilliger et al. 2013; 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)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ALLOCATIONS; ATOMS; CHAINS; CRYSTALS; CURRENTS; DEFORMATION; DENSITY; ELECTRON DENSITY; ELECTRONS; JOINTS; MOLECULES; RESOLUTION