November 2013 issue
Proceedings of the CCP4 study weekend edited by Pietro Roversi, Helen Walden and Charles Ballard
Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed.
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.
Processing of NMR structures for molecular replacement by AMPLE works well.
Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed.
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.
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.
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.
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.
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.
Under favourable circumstances, density modification and polyalanine tracing with SHELXE can be used to improve and validate potential solutions from molecular replacement.
An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented.
The use of molecular replacement in solving the structures of G protein-coupled receptors is discussed, with specific examples being described in detail.