ProSMART Tutorial

Generation Of ProSMART External Restraints
And Use In Crystallographic Refinement By REFMAC5

Rob Nicholls - nicholls@mrc-lmb.cam.ac.uk
Paul Emsley - pemsley@mrc-lmb.cam.ac.uk
Garib Murshudov - garib@mrc-lmb.cam.ac.uk

Introduction

In this tutorial, the generation and usage of ProSMART external restraints will be demonstrated using the 3.5Å structure 1ryx as an example. We will cover generating restraints to a homologous higher-resolution structure (2d3i, 2.15Å), and secondary structure restraints representing hydrogen bonding patterns. Other restraint types that are available through ProSMART include fragment-based helical restraints, general reference fragment-based restraints, and self-restraints.

We will also use ProSMART for structural analysis in the context of crystallographic refinement, in order to gain intuition about the local conformational state of the model before and after refinement with external restraints, and see how this information can be used to aid the model building/refinement procedure.

Tutorial

• Part 1 - restraining a low-resolution structure using a homologous higher-resolution reference model.
• Part 2 - analysis of structural changes that occur during refinement (and differences between homologues).
• Part 2a - ProSMART structural analysis with PyMOL.
• Part 2b - ProSMART structural analysis with CCP4mg.
• Part 3 - hydrogen bond type secondary structure restraints (for when there's no good homologous model).

Links

Here are a few key resources:

ProSMART:
• Conformation-independent structural comparison of macromolecules with ProSMART (2014)
• An Overview of ProSMART (2012)
• Conformation-independent comparison of protein structures (2011)

Low resolution refinement with REFMAC5 and ProSMART:
• Recent Advances in Low Resolution Refinement Tools in REFMAC5 (2013)
• Low Resolution Refinement Tools in REFMAC5 (2012)

REFMAC5:
• REFMAC5 for the refinement of macromolecular crystal structures (2011)

Other resources:
• List of ProSMART Keywords
• Computational Crystallography Group Homepage