dr. Eugene Krissinel & dr. Lucrezia Catapano, tutor
CCP4 core group, UK
&
MRC Laboratory of Molecular Biology
Cambridge, UK
HT3: Processing & Structure determination
T1 (Tutorial): Automatic and Fundamental Molecular Replacement
Molecular Replacement (MR) is the most popular method to solve the Phase Problem nowadays. MR is based on the assumption that target structure has a highly similar structural homologue, which may be found by, e.g. matching target’s sequence to sequences of known structures. In this method, a sufficiently close molecular model is positioned (i.e., rotated and translated) in crystal coordinates such that calculated structure amplitudes reproduce experimental results in the best possible way. Then, calculated phases are considered as first approximations to real phases, which allow for subsequent model building, refinement and phase improvement.
For the success of Molecular Replacement, the MR model should be sufficiently similar to the target structure. In this tutorial, we will discuss how to find and prepare suitable MR Search Models (including working with Alphafold2 predicted models) for use in molecular replacement programs (Phaser and Molrep). We will also cover the basic principles of MR and the software available in CCP4 for each step of MR, including both fundamental tools and automatic pipelines that combine all needful steps and can deliver phased structure starting from experimental observation and sequence – or even without the later.
