X-ray structure determination at low resolution.
As an example of structure determination in the 3.5-4.5 A resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alone was subsequently solved at 3 A resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at approximately 4 A resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.
Brunger
Axel T
AT
Howard Hughes Medical Institute, Stanford University, USA. brunger@stanford.edu
DeLaBarre
Byron
B
Davies
Jason M
JM
Weis
William I
WI
D000251:Adenosine Triphosphatases / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular
D000251:Adenosine Triphosphatases