October 2001 issue
Molecular replacement and its relatives
Proceedings of the CCP4 study weekend
The use of likelihood, particularly a multivariate likelihood function for multiple molecular-replacement models, allows difficult molecular-replacement problems to be solved more easily.
The locked rotation and translation functions are a powerful way of taking advantage of the presence of non-crystallographic symmetry in a structure determination by the molecular-replacement method.
The principles and the implementation of the molecular-replacement procedures in CNS are reviewed.
Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the E. coli colicin immunity protein Im7; the other is the previously unreported crystal structure of the carboxy-terminal SH2 domain from the p85α subunit of human phosphatidylinositol 3-OH kinase complexed to a PDGF receptor-derived specificity peptide.
This review summarizes the steps required to exploit electron-microscopy images as models for molecular replacement, indicating some of the associated practical problems.
The paper describes the structure solution of UDP-galactopyranomutase. The structure solution relied on the placement of experimental density into a new crystal form.
Mathematical data mining is used to generate a representative set of protein fragments to use as search models in molecular replacement.
The proposal is investigated that protein tertiary structure prediction methods and threading methods in particular might be applied to the problem of solving a protein structure by X-ray crystallography.
The molecular-replacement method has been extended to locate macromolecular fragments in an electron-density map using a spherically averaged phased translation and a phased rotation function.
An overview of the use of NMR models to solve crystal structures by molecular replacement is presented with particular emphasis on the preparation of search models. A recently developed protocol is tested and found to offer good results.
The anomalous signal of S atoms can contribute to many aspects of solving protein structures and should be used routinely. For example, the anomalous scattering of sulfur was essential to solve the structure of trypsin which was initially phased from a single intrinsic Ca2+ ion in an SAS diffraction experiment.