Dear Stefan, Did you have a look at the NCS related helices? To me it looks like your NCS restraints on B-factors are too strong, or not valid for your crystal packing.
Best, Herman ________________________________ Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Stefan Gajewski Gesendet: Mittwoch, 24. Juli 2013 07:18 An: [email protected] Betreff: Re: [ccp4bb] Where to cut the data in this medium resolution dataset Nat, What do "correct" B-factors look like? What refinement strategy did you use for them? 1) If I see strong positive density in the Fo-Fc map along the backbone of two turns of an correctly placed alpha helix, therefore the B-factors are too high in that region. The model after refinement suggest less scattering in that region than is observed which is most likely explained by incorrectly high B-factors. 2) xyz, TLS and individual B-factors (no grouping). SS and ramachandran restraints on coordinates and NCS restraints on coordinates and B-factors. Note that the R-free value in the 3.4A shell is lower than the R-work (and also the Rpim in that shell!) which clearly indicates this refinement was not stable. I don't think it indicates anything about the "stability" of refinement - my guess would be that the NCS is biasing R-free. I suppose it could also indicate that the data in the 3.6-3.4 range are basically noise, although if the maps look better then that would suggest the opposite. I think the refinement is not parametrized correctly. Thank you, S.
