Lecture 4

Macromolecular structure determination by X-ray crystallography

Aims

• To introduce some of the concepts in macromolecular X-ray crystallography.
• To raise some of the issues that structural bioinformaticians should be aware of when working with structures determined by X-ray crystallography.

Objectives

After this lecture you will be able to:

• describe how electron density maps are represented;
• implement an algorithm for skeletonizing an electron density map;
• describe how an alpha-carbon trace can be constructed;
• discuss concepts related to model quality of X-ray structures;
• discuss difficulties in interpreting X-ray structures.

Supplementary Material

Some of the lecture slides are available on-line (1 per page, 4 per page, local scanned copy).

Articles mentioned in the lecture include:

• J. Greer (1974) Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins. J. Mol. Biol., 82, 279-301. doi:10.1016/0022-2836(74)90591-9
• J. M. Word, S. C. Lovell, J. S. Richardson and D. C. Richardson (1998) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285, 173-1747. doi:10.1006/jmbi.1998.2401

There are many excellent eductional resources on X-ray crystallography, including:

• Diving into the heart of the molecules of life (video), by Claude Sauter
• A Glossary of Terms from Crystallography, NMR, and Homology Modeling by Gale Rhodes
• Protein Crystallography Course at the University of Cambridge, particularly
  • Overview of macromolecular X-ray crystallography by Randy Read
  • Introduction to fitting, refinement and validation by Randy Read
  • Fitting, Refinement & Validation by Phil Evans
• A Brief Introduction to Protein Crystallography by Dave Lawson
• Crystallography 101 by Bernhard Rupp
• A Non-Mathematical Introduction to X-ray Diffraction by Charles A. Taylor
• Kevin Cowtan's Picture Book of Fourier Transforms