Literature DB >> 11567161

Multidimensional molecular replacement.

N M Glykos1, M Kokkinidis.   

Abstract

A method is described which attempts to simultaneously and independently determine the positional and orientational parameters of all molecules present in the asymmetric unit of a target crystal structure. This is achieved through a reverse Monte Carlo optimization of a suitable statistic (such as the R factor or the linear correlation coefficient between the observed and calculated amplitudes of the structure factors) in the 6n-dimensional space defined by the rotational and translational parameters of the n search models. Results from the application of this stochastic method - obtained with a space-group-general computer program which has been developed for this purpose - indicate that with present-day computing capabilities the method may be applied successfully to molecular-replacement problems for which the target crystal structure contains up to three molecules per asymmetric unit. It is also shown that the method may be useful in cases where the assumption of topological segregation of the self- and cross-vectors in the Patterson function is violated (as may happen, for example, in closely packed crystal structures).

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Substances:

Year:  2001        PMID: 11567161     DOI: 10.1107/s0907444901008563

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  6 in total

1.  Purification, crystallization and preliminary X-ray diffraction analysis of a variant of the ColE1 Rop protein.

Authors:  Maria Ambrazi; George Fellas; Evangelia G Kapetaniou; Dina Kotsifaki; Mary Providaki; Michael Kokkinidis
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2008-04-30

2.  MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

Authors:  Jouko J Virtanen; Yang Zhang
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-06-08       Impact factor: 7.652

3.  Protein Crystallography from the Perspective of Technology Developments.

Authors:  Xiao-Dong Su; Heng Zhang; Thomas C Terwilliger; Anders Liljas; Junyu Xiao; Yuhui Dong
Journal:  Crystallogr Rev       Date:  2015       Impact factor: 2.467

Review 4.  Implications of AlphaFold2 for crystallographic phasing by molecular replacement.

Authors:  Airlie J McCoy; Massimo D Sammito; Randy J Read
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-01-01       Impact factor: 7.652

5.  Solving structures of protein complexes by molecular replacement with Phaser.

Authors:  Airlie J McCoy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-12-13

6.  An introduction to molecular replacement.

Authors:  Philip Evans; Airlie McCoy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05
  6 in total

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