Open AccessX‐ray structure determination at low resolution
Author(s) -
Brunger Axel T.,
DeLaBarre Byron,
Davies Jason M.,
Weis William I.
Publication year - 2009
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444908043795
Subject(s) - resolution (logic) , low resolution , high resolution , tandem , crystallography , domain (mathematical analysis) , homology modeling , diffraction , fragment (logic) , chemistry , physics , computer science , mathematics , algorithm , materials science , optics , nuclear magnetic resonance , artificial intelligence , geology , mathematical analysis , remote sensing , composite material , enzyme
As an example of structure determination in the 3.5–4.5 Å 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 Å 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 ∼4 Å 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.