Introduction to X-ray Crystallography

Introduction to X-ray Crystallography

Protein structure determination using X-ray crystallography is the major experimental technique in Structural Biology. This module will provide an in-depth introduction to diffraction techniques, covering the basics of symmetry, diffraction and methods for measuring the diffraction pattern, as well as the mathematical techniques for solving and refining a crystal structure. No similar module is offered at this level anywhere in South Africa.


Dr Muhammed Sayed, Department of Biotechnology (UWC), is a protein crystallographer who completed his post-doctoral studies under Professor Tom Blundell at Cambridge University. He will supervise the web-courses in protein structure and protein crystallography. His goal is to develop protein crystallography as a practical discipline.

Main Outcomes

The aim of this section of this module is to introduce students to the principles of X-ray diffraction and the elucidation of crystal structures. It is intended to underpin and to accompany students' independent study of the Protein Crystallography web-based course. On completion of this module, students should be well prepared for the module on "Protein Crystallography" later in the course.

The ability to:

  • crystallize proteins,
  • collect and process crystallographic data,
  • determine space groups,
  • solve structures by molecular replacement,
  • solve structures by isomorphous replacement and multiple anomalous dispersion techniques
  • display structures
  • build models of proteins using experimentally determined maps
  • use standard crystallographic software

Main Content

  1. Crystals
    1. Crystal growth
    2. Periodicity and unit cells
  2. Symmetry
    1. Symmetry elements, point groups and space groups
  3. Diffraction
    1. Introduction to diffraction of waves
    2. The reciprocal lattice
    3. Diffraction by crystals; Bragg equation
    4. Fourier transforms
  4. Obtaining the diffraction pattern
    1. Instruments
    2. Data collection strategies
    3. The phase problem
  5. Deriving a trial structure
    1. Direct methods
    2. Patterson method
    3. Isomorphous replacement
    4. Anomalous scattering
  6. Refining the structure
    1. Fourier and least-squares methods
  7. Analysis of structural parameters

Online Lectures


Tutorial worksheets will be handed out at regular intervals. These must be completed and handed in by the specified deadlines. A 2 hour examination will be given at the end of the module. The worksheets and exam will count 40 and 60% respectively.



A number of helpful books are available in the UCT and UWC libraries. Useful introductory texts include:

Blake, AJ, JM Cole, JSO Evans, P Main, S Parsons, and DJ Watkin. 2009. Crystal Structure Analysis: Principles and Practice. Oxford; New York: Oxford University Press.

Blow, D. 2002. Outline of Crystallography for Biologists. Oxford; New York: Oxford University Press.

Glusker, JP and KN Trueblood. 2010. Crystal Structure Analysis: A Primer. Oxford; New York: Oxford University Press.

Hammond, C. 1992. Introduction to Crystallography. Oxford: Oxford University Press.

The International Union of Crystallography website (mirrored at has numerous useful articles.