Maybe a few remarks might help:
Ad a) R merge of 80% may be OK if I/sig for high res shell is >2. What rationale is that statement based upon and what is the exact meaning of this statement? Is an Rmerge of 80% not ok when <I/sigi> is say < 1.5? Or would 80% be ok if the <i/sigI> is 3.0? Why should an R-merge of 80% be (too) high in the first place? b) there is no statistical justification whatsoever for the <I/sigI> cutoff of 2 for refinement. This has been discussed @CCP4bb multiple times, for good reason. In this particular case, the (in)completeness appears to be the dominating factor. c) as Pavel notes, the R-value improvement means nil when truncating data - try to refine from 8 to 2 A and Rs might be even lower (abuse we engaged in ages ago when we did not know better and no ML) d) absolute values of refinement Rs vs (historic) expectation values cannot be judged without complete and detailed knowledge of the refinement protocol. The ultimate question is whether your model improves with inclusion of more data or not. Kay Diederichs has a few papers to this effect that make good reading. And CC1/2 seems to provide statistically justifiable limits for cut-off of (reasonably complete) high resolution shells. LG, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Emily Golden Sent: Dienstag, 27. August 2013 07:48 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution, R factors and data quality Thanks Yuriy and Pavel, at this resolution one would expect R/Rfree to be ~ 10-11%/12-13% assuming you applied anisotropic B-factor refinement ( and probably having a low symmetry SG). R merge of 80% may be OK if I/sig for high res shell is >2. Yes, I used anisotropic Bfactors and the space group is P1 21 1. However, the I/sig is only 1.5 in the highest shell. Cutting the data such that the I/sig is >2 has improved the R factors. Thank you. Maps get worse.... Could it be when you use all resolution range you get 59% of missing reflections in highest resolution shell filled in with DFc for the purpose of map calculation? Yes! the map that I was looking at was filled. Emily On 27 August 2013 09:49, Emily Golden <10417...@student.uwa.edu.au> wrote: Hi All, I have collected diffraction images to 1 Angstrom resolution to the edge of the detector and 0.9A to the corner. I collected two sets, one for low resolution reflections and one for high resolution reflections. I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A shell. However, my Rmerge in the highest shelll is not good, ~80%. The Rfree is 0.17 and Rwork is 0.16 but the maps look very good. If I cut the data to 1 Angstrom the R factors improve but I feel the maps are not as good and I'm not sure if I can justify cutting data. So my question is, should I cut the data to 1Angstrom or should I keep the data I have? Also, taking geometric restraints off during refinement the Rfactors improve marginally, am I justified in doing this at this resolution? Thank you, Emily
