Molecular replacements

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.

Molecular replacement: tricks and treats

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.

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

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

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

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.

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

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

Advances in Rosetta structure prediction for difficult molecular-replacement problems

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

Improved estimates of coordinate error for molecular replacement

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.

SCEDS: protein fragments for molecular replacement in Phaser

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.

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

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.

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

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.

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.

Extending molecular-replacement solutions with SHELXE

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

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

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

Molecular replacement then and now

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

Phaser.MRage: automated molecular replacement

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

Applications of molecular replacement to G protein-coupled receptors

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