Postgraduate Certificate:
Techniques in Structural Molecular Biology (TSMB)

Prospective students

bullet Course overview
bullet Course details
bullet Syllabus
bullet Fees
bullet How to apply

Related links

bullet MSc structural biology
bullet PPS course
bullet PX course
bullet TSMB course
bullet Commonwealth
bullet scholarships

Current TSMB students
[Restricted access]

bullet TSMB students 2009/10
bullet TSMB students 2008/9

 

Distance Learning: Techniques in Structural Molecular Biology (TSMB)

Postgraduate Certificate

TSMB Syllabus

 

Section 10: Analysing the Structure

This section gives a quick introduction to the analysis of experimentally determined structures, including the checking for possible errors.

  • Introduction
  • Structures as "models"

Models from X-ray Crystallography
Models from NMR

  • Estimation of errors

Precision vs. accuracy
Error Estimation in X-ray Crystallography
Estimation of Standard Uncertainties
Parameters: Resolution, R Factor, Average Positional Error, Atomic B Factor
Selecting X-ray Crystal Structures
Error Estimation in NMR
Global Parameters: Restraints, r.m.s.d., NMR "R Factor"
Selecting NMR Structures

  • Errors in deposited structures

Typical errors (uncertainties)
Serious errors

  • Stereochemical parameters

Protein parameters
The Ramachandran Plot
Side Chain Torsion Angles
Bad Contacts
DNA and Ligand parameters

  • Software for Quality Checks
  • Quality assignments available on the Web

PDBsum and PROCHECK
WHATCHECK
Validation servers

 

Objectives

To make students aware that 3D structures of proteins, and DNA, are models that aim to satisfy the experimental data. As such, they can contain errors for a variety of reasons. So the interpretations and conclusions drawn from any 3D structure must take this into consideration. At the end of this section, students should:

  • Appreciate the likely differences in the quality of different macromolecular structures
  • To be familiar with various approaches for identifying different types of errors
  • To be aware of the commonly used programs and Web sites for assessing structural quality