Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 11 (November 2013)


Molecular replacements

Proceedings of the CCP4 study weekend

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


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Solving nucleic acid structures by molecular replacement (p. 2174).

introduction


 

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Acta Cryst. (2013). D69, 2165-2166  [ doi:10.1107/S0907444913027352 ]

Molecular replacements

C. Ballard, P. Roversi and H. Walden

Synopsis: An introduction to the proceedings of the CCP4 Study Weekend held at the East Midlands Conference Centre of the University of Nottingham, England, in January 2013.

Online 18 October 2013


research papers


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Acta Cryst. (2013). D69, 2167-2173  [ doi:10.1107/S0907444913015291 ]

Molecular replacement: tricks and treats

C. Abergel

Synopsis: To be successful, molecular replacement relies on the quality of the model and of the crystallographic data. Some tricks that could be applied to the models or to the crystal to increase the success rate of MR are discussed here.

Online 12 October 2013


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Acta Cryst. (2013). D69, 2174-2185  [ doi:10.1107/S0907444913013218 ]

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

M. Marcia, E. Humphris-Narayanan, K. S. Keating, S. Somarowthu, K. Rajashankar and A. M. Pyle

Synopsis: Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed.

Online 12 October 2013


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

Acta Cryst. (2013). D69, 2186-2193  [ doi:10.1107/S0907444913027157 ]

An estimated 5% of new protein structures solved today represent a new Pfam family

J. Mistry, E. Kloppmann, B. Rost and M. Punta

Synopsis: This study uses the Pfam database to show that the sequence redundancy of protein structures deposited in the PDB is increasing. The possible reasons behind this trend are discussed.

Online 12 October 2013


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

Acta Cryst. (2013). D69, 2194-2201  [ doi:10.1107/S0907444913018453 ]

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden

Synopsis: Processing of NMR structures for molecular replacement by AMPLE works well.

Online 12 October 2013


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Acta Cryst. (2013). D69, 2202-2208  [ doi:10.1107/S0907444913023305 ]

Advances in Rosetta structure prediction for difficult molecular-replacement problems

F. DiMaio

Synopsis: Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed.

Online 12 October 2013


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Acta Cryst. (2013). D69, 2209-2215  [ doi:10.1107/S0907444913023512 ]

Improved estimates of coordinate error for molecular replacement

R. D. Oeffner, G. Bunkóczi, A. J. McCoy and R. J. Read

Synopsis: A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded.

Online 12 October 2013


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

Acta Cryst. (2013). D69, 2216-2225  [ doi:10.1107/S0907444913021811 ]

SCEDS: protein fragments for molecular replacement in Phaser

A. J. McCoy, R. A. Nicholls and T. R. Schneider

Synopsis: Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments.

Online 4 October 2013


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Acta Cryst. (2013). D69, 2226-2235  [ doi:10.1107/S0907444913011438 ]

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

D. L. Makino and E. Conti

Synopsis: The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement.

PDB reference: 4ifd

Online 12 October 2013


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Acta Cryst. (2013). D69, 2236-2243  [ doi:10.1107/S0907444913018593 ]

Building a pseudo-atomic model of the anaphase-promoting complex

K. Kulkarni, Z. Zhang, L. Chang, J. Yang, P. C. A. da Fonseca and D. Barford

Synopsis: This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data.

Online 12 October 2013


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Acta Cryst. (2013). D69, 2244-2250  [ doi:10.1107/S0907444913017770 ]

Model morphing and sequence assignment after molecular replacement

T. C. Terwilliger, R. J. Read, P. D. Adams, A. T. Brunger, P. V. Afonine and L.-W. Hung

Synopsis: 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.

Online 18 October 2013


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Acta Cryst. (2013). D69, 2251-2256  [ doi:10.1107/S0907444913027534 ]

Extending molecular-replacement solutions with SHELXE

A. Thorn and G. M. Sheldrick

Synopsis: Under favourable circumstances, density modification and polyalanine tracing with SHELXE can be used to improve and validate potential solutions from molecular replacement.

Online 18 October 2013


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Acta Cryst. (2013). D69, 2257-2265  [ doi:10.1107/S0907444913022336 ]

From lows to highs: using low-resolution models to phase X-ray data

D. I. Stuart and N. G. A. Abrescia

Synopsis: An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented.

Online 18 October 2013


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Acta Cryst. (2013). D69, 2266-2275  [ doi:10.1107/S0907444913011426 ]

Molecular replacement then and now

G. Scapin

Synopsis: A brief overview, with examples, of the evolution of molecular-replacement methods and models over the past few years is presented.

Online 18 October 2013


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Acta Cryst. (2013). D69, 2276-2286  [ doi:10.1107/S0907444913022750 ]

Phaser.MRage: automated molecular replacement

G. Bunkóczi, N. Echols, A. J. McCoy, R. D. Oeffner, P. D. Adams and R. J. Read

Synopsis: The functionality of the molecular-replacement pipeline phaser.MRage is introduced and illustrated with examples.

Online 18 October 2013


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Acta Cryst. (2013). D69, 2287-2292  [ doi:10.1107/S090744491301322X ]

Applications of molecular replacement to G protein-coupled receptors

A. C. Kruse, A. Manglik, B. K. Kobilka and W. I. Weis

Synopsis: The use of molecular replacement in solving the structures of G protein-coupled receptors is discussed, with specific examples being described in detail.

Online 18 October 2013


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