Crystallographic refinement of ricin to 2.5 A.
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.
Rutenber
E
E
Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.
Katzin
B J
BJ
Ernst
S
S
Collins
E J
EJ
Mlsna
D
D
Ready
M P
MP
Robertus
J D
JD
D003461:Crystallography; D006023:Glycoproteins / Q000737:chemistry*; D016018:Least-Squares Analysis; D046911:Macromolecular Substances; D008432:Mathematical Computing; D008958:Models, Molecular; D011487:Protein Conformation; D011952:Receptors, Concanavalin A; D012276:Ricin / Q000737:chemistry*; D012984:Software
D006023:Glycoproteins; D046911:Macromolecular Substances; D011952:Receptors, Concanavalin A; D012276:Ricin