Crystallographic refinement of ricin to 2.5 A

Proteins. 1991;10(3):240-50. doi: 10.1002/prot.340100308.

Abstract

The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Crystallography
  • Glycoproteins / chemistry*
  • Least-Squares Analysis
  • Macromolecular Substances
  • Mathematical Computing
  • Models, Molecular*
  • Protein Conformation
  • Receptors, Concanavalin A
  • Ricin / chemistry*
  • Software

Substances

  • Glycoproteins
  • Macromolecular Substances
  • Receptors, Concanavalin A
  • Ricin