Acta Crystallographica Section D

Biological Crystallography

Volume 64, Part 1 (January 2008)


Molecular replacement

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Using an EM map as a model for molecular replacement. Left: an EM map of yeast fatty acid synthase (FAS) at 24 Å resolution. Right: an X-ray crystal structure of FAS determined at 4 Å resolution. Bottom: a schematic representation of the lipid bilayer whose major component is the fatty acid synthesized by FAS (p. 76).

research papers


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Acta Cryst. (2008). D64, 1-10  [ doi:10.1107/S0907444907051554 ]

An introduction to molecular replacement

P. Evans and A. McCoy

Synopsis: An outline is given of the basic features of the molecular-replacement method for solving crystal structures.

Online 4 December 2007


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Acta Cryst. (2008). D64, 11-16  [ doi:10.1107/S0907444907044460 ]

AMoRe: classical and modern

S. Trapani and J. Navaza

Synopsis: An account is given of the latest developments of the AMoRe package.

Online 4 December 2007


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Acta Cryst. (2008). D64, 17-24  [ doi:10.1107/S0907444907049736 ]

The befores and afters of molecular replacement

E. Dodson

Synopsis: This review outlines questions to consider when attempting to solve crystal structures by molecular replacement.

Online 4 December 2007


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Acta Cryst. (2008). D64, 25-32  [ doi:10.1107/S0907444907046343 ]

Sequence alignment for molecular replacement

G. J. Barton

Synopsis: The problems of gaining accurate protein sequence alignments for molecular replacement are discussed, current techniques explained and strategies suggested.

Online 4 December 2007


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Acta Cryst. (2008). D64, 33-39  [ doi:10.1107/S0907444907049839 ]

Model preparation in MOLREP and examples of model improvement using X-ray data

A. A. Lebedev, A. A. Vagin and G. N. Murshudov

Synopsis: The default model-preparation scheme of MOLREP is described. Two examples are presented of model improvement using X-ray data.

Online 4 December 2007


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Acta Cryst. (2008). D64, 40-48  [ doi:10.1107/S0907444907053516 ]

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

M. Delarue

Synopsis: The possibility of taking into account large-amplitude collective movements of a given model by using a subset of low-frequency normal modes is evaluated for molecular replacement and refinement using X-ray data or cryo-EM maps.

Online 4 December 2007


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Acta Cryst. (2008). D64, 49-60  [ doi:10.1107/S0907444907047580 ]

ARP/wARP and molecular replacement: the next generation

S. X. Cohen, M. Ben Jelloul, F. Long, A. Vagin, P. Knipscheer, J. Lebbink, T. K. Sixma, V. S. Lamzin, G. N. Murshudov and A. Perrakis

Synopsis: A systematic test shows how ARP/wARP deals with automated model building for structures that have been solved by molecular replacement. A description of protocols in the flex-wARP control system and studies of two specific cases are also presented.

Online 4 December 2007


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Acta Cryst. (2008). D64, 61-69  [ doi:10.1107/S090744490705024X ]

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. H. Zwart, L.-W. Hung, R. J. Read and P. D. Adams

Synopsis: The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods.

Online 4 December 2007


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Acta Cryst. (2008). D64, 70-75  [ doi:10.1107/S0907444907053334 ]

Combining X-ray and electron-microscopy data to solve crystal structures

J. Navaza

Synopsis: Overview and examples of combined use of X-ray and electron-microscopy data.

Online 4 December 2007


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Acta Cryst. (2008). D64, 76-82  [ doi:10.1107/S090744490705398X ]

From electron microscopy to X-ray crystallography: molecular-replacement case studies

Y. Xiong

Synopsis: Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement using various standard MR packages such as AMoRe, MOLREP and Phaser.

Online 4 December 2007


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Acta Cryst. (2008). D64, 83-89  [ doi:10.1107/S0907444907033938 ]

Fitting molecular fragments into electron density

K. Cowtan

Synopsis: A number of techniques for the location of small and medium-sized model fragments in experimentally phased electron-density maps are explored. The application of one of these techniques to automated model building is discussed.

Online 4 December 2007


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Acta Cryst. (2008). D64, 90-98  [ doi:10.1107/S0907444907053802 ]

NCS-constrained exhaustive search using oligomeric models

M. N. Isupov and A. A. Lebedev

Synopsis: Three difficult MR cases are reported in which the orientation of a search oligomer or its internal parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches. Such an exhaustive search was feasible because of constraints on the model parameters derived from the self-rotation function.

Online 4 December 2007


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2008). D64, 99-107  [ doi:10.1107/S090744490705531X ]

Surprises and pitfalls arising from (pseudo)symmetry

P. H. Zwart, R. W. Grosse-Kunstleve, A. A. Lebedev, G. N. Murshudov and P. D. Adams

Synopsis: The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.

Online 4 December 2007


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Acta Cryst. (2008). D64, 108-118  [ doi:10.1107/S0907444907054923 ]

Type II dehydroquinase: molecular replacement with many copies

K. A. Stewart, D. A. Robinson and A. J. Lapthorn

Synopsis: The type II dehydroquinase enzyme is a symmetrical dodecameric protein which crystallizes in either high-symmetry cubic space groups or low-symmetry crystal systems with multiple copies in the asymmetric unit. Both systems have provided challenging examples for molecular replacement; for example, a triclinic crystal form has 16 dodecamers (192 monomers) in the unit cell. Three difficult examples are discussed and two are used as test cases to compare the performance of four commonly used molecular-replacement packages.

Online 4 December 2007


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Acta Cryst. (2008). D64, 119-124  [ doi:10.1107/S0907444907037195 ]

MrBUMP: an automated pipeline for molecular replacement

R. M. Keegan and M. D. Winn

Synopsis: An automation pipeline for macromolecular structure solution by molecular replacement with a special emphasis on the discovery and preparation of a large number of search models is described.

Online 4 December 2007


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Acta Cryst. (2008). D64, 125-132  [ doi:10.1107/S0907444907050172 ]

BALBES: a molecular-replacement pipeline

F. Long, A. A. Vagin, P. Young and G. N. Murshudov

Synopsis: The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problems using only input X-ray and sequence data.

Online 4 December 2007


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Acta Cryst. (2008). D64, 133-140  [ doi:10.1107/S0907444907050111 ]

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

R. Schwarzenbacher, A. Godzik and L. Jaroszewski

Synopsis: The practical limits of molecular replacement can be extended by using several specifically designed protein models based on fold-recognition methods and by exhaustive searches performed in a parallelized pipeline. Updated results from the JCSG MR pipeline, which to date has solved 33 molecular-replacement structures with less than 35% sequence identity to the closest homologue of known structure, are presented.

Online 4 December 2007


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