I can't help but suggest to also try PDB_REDO for tuning refinement. http://xtal.nki.nl/PDB_REDO/index.jsp
One of the things you get, is exactly what Pavel explains below, how your structure looks in comparison with others in similar resolution, but also with the PDB_REDO data bank structures. I will also agree that the 90% complete data set might be best - just refine both models, compare, and choose the best one according to validation criteria (you get a few for free in PDB_REDO and of course in eg Molprobity) Tassos Sent from my iPad > On 22 Feb 2014, at 02:20, Pavel Afonine <pafon...@gmail.com> wrote: > > Chris, > > what you get is not unheard of but clearly you are not in majority: at around > 1.95A resolution distribution of R-factors in PDB is: > > Histogram of Rwork for models in PDB at resolution 1.85-2.05 A: > 0.093 - 0.118 : 3 > 0.118 - 0.143 : 75 > 0.143 - 0.168 : 821 > 0.168 - 0.193 : 2617 > 0.193 - 0.218 : 2950 > 0.218 - 0.242 : 1147 > 0.242 - 0.267 : 201 <<< your case > 0.267 - 0.292 : 21 > 0.292 - 0.317 : 2 > 0.317 - 0.342 : 1 > Histogram of Rfree for models in PDB at resolution 1.85-2.05 A: > 0.138 - 0.160 : 12 > 0.160 - 0.183 : 106 > 0.183 - 0.205 : 742 > 0.205 - 0.227 : 1971 > 0.227 - 0.249 : 2566 > 0.249 - 0.272 : 1676 > 0.272 - 0.294 : 616 > 0.294 - 0.316 : 119 <<< your case > 0.316 - 0.339 : 24 > 0.339 - 0.361 : 6 > Histogram of Rfree-Rwork for all model in PDB at resolution 1.85-2.05 A: > 0.001 - 0.011 : 67 > 0.011 - 0.021 : 428 > 0.021 - 0.031 : 1324 > 0.031 - 0.041 : 2220 > 0.041 - 0.050 : 1975 > 0.050 - 0.060 : 1059 <<< your case > 0.060 - 0.070 : 459 > 0.070 - 0.080 : 201 > 0.080 - 0.090 : 75 > 0.090 - 0.100 : 30 > > Pavel > > P.S.: Command to the statistics as above is: > phenix.r_factor_statistics 1.95 > > >> On Fri, Feb 21, 2014 at 4:41 PM, Chris Fage <cdf...@gmail.com> wrote: >> Dear CCP4BB Users, >> >> I recently collected a number of datasets from plate-shaped crystals >> that diffracted to 1.9-2.0 angstroms and yielded very nice electron >> density maps. There is no major density unaccounted for by the model; >> however, I am unable to decrease Rwork and Rfree beyond ~0.25 and >> ~0.30, respectively. Probably due to the more 2-dimensional nature of >> my crystals, there is a range of phi angles in which the reflections >> are smeared, and I am wondering if the problem lies therein. >> >> I would be grateful if anyone could provide advice for improving my >> refinement statistics, as I was under the impression that the >> R-factors should be ~5% lower for the given resolution. >> >> A few more pieces of information: >> -Space group = P21, with 2 monomers per asymmetric unit; >> -Chi square = 1.0-1.5; >> -Rmerge = 0.10-0.15; >> -Data were processed in HKL2000 and refined in Refmac5 and/or phenix.refine; >> -PHENIX Xtriage does not detect twinning, but hints at possible weak >> translational pseudosymmetry; >> -I was previously able to grow one atypically thick crystal which >> diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22. >> Unfortunately, the completeness of the dataset was only ~90%. >> >> Regards, >> Chris >
