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      Solving structures of protein complexes by molecular replacement with Phaser

      a , *

      Acta Crystallographica Section D: Biological Crystallography

      International Union of Crystallography

      Crystallography of complexes

      macromolecular crystallography, molecular replacement, maximum likelihood

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          Abstract

          Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described.

          Abstract

          Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models ( i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

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          Author and article information

          Conference
          Acta Crystallogr D Biol Crystallogr
          Acta Cryst. D
          Acta Crystallographica Section D: Biological Crystallography
          International Union of Crystallography
          0907-4449
          1399-0047
          01 January 2007
          13 December 2006
          13 December 2006
          : 63
          : Pt 1 ( publisher-idID: d070100 )
          : 32-41
          Affiliations
          [a ]University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England
          Author notes
          Correspondence e-mail: ajm201@ 123456cam.ac.uk
          Article
          ba5095 ABCRE6 S0907444906045975
          10.1107/S0907444906045975
          2483468
          17164524
          © International Union of Crystallography 2007

          This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.

          Crystallography of complexes
          Categories
          Research Papers

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