Lecture 5

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 (PDF).

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

• 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
• Book of Fourier by Kevin Cowtan