Dear Michael, Did you ask Phaser to check for all possible space groups? There are still I422 and I4 you did not mention. If the space group that came out of Phaser is different from the space group used for processing, subsequent refinement programs may use the wrong space group from the processing. This should be easy to check.
The other suggestion I have is to try a different processing program. Although XDS is excellent, I find that sometimes it has difficulties with ice rings, which reveal themselves not in the processing, but in the subsequent refinement. You may want to try Mosflm or some other processing program. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Michael Jarva Gesendet: Sonntag, 15. Oktober 2017 03:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Another troublesome dataset (High Rfree after MR) To add to the current anisotropic discussion I recently got a dataset I'm unable to refine and I'm hoping I could get some help on figuring out if there's anything I can do. I get a clear cut solution with Phaser using the same protein as search model and got a TFZ of >16, LLG >200, and a packing that makes sense, so I don't doubt the solution. However, the maps look terrible, more like something I would expect from a 3.65Å dataset rather than the 2.65Å it supposedly is. The dataset merges well in I4122 to 2.65Å with an overall Rmerge of 5% and a CC1/2 of >0.5 in the outer shell (see the bottom for full summary). There is some minor radiation damage but I could cut out most of it due to the high symmetry. Xtriage reports no indication of twinning, but does say that the data is moderately anisotropic, so I ran the unmerged data through the StarAniso server, which reported the ellipsoidal resolution limits to be 2.304, 2.893, and 3.039. Refining with the anisotropically truncated data improves the maps somewhat, but I am still unable to get the Rfree below 38%. I tried using both phenix.refine and buster with similar results. I've considered the choice of space group and tried I41, F222, I212121 , and C2, but with the same results, and Zanuda tells me the same thing. Lastly, there is some minor ice rings, so my last try was to exclud the ice ring resolutions, but this made little to no difference. Normally I would just write this off as the data being bad but this time all the statistics tell me this should be doable so I'm curious what has gone wrong. Cheers Michael Jarva Summary data for Project: XDSproject Crystal: XDScrystal Dataset: XDSdataset Overall InnerShell OuterShell Low resolution limit 34.87 34.87 2.78 High resolution limit 2.65 8.79 2.65 Rmerge (within I+/I-) 0.052 0.026 1.595 Rmerge (all I+ and I-) 0.057 0.030 1.805 Rmeas (within I+/I-) 0.062 0.031 1.924 Rmeas (all I+ & I-) 0.063 0.033 1.993 Rpim (within I+/I-) 0.032 0.017 1.042 Rpim (all I+ & I-) 0.025 0.014 0.817 Rmerge in top intensity bin 0.030 - - Total number of observations 19931 566 2681 Total number unique 3597 114 471 Mean((I)/sd(I)) 11.3 42.3 0.8 Mn(I) half-set correlation CC(1/2) 0.999 0.999 0.575 Completeness 97.9 93.1 99.6 Multiplicity 5.5 5.0 5.7 Anomalous completeness 92.4 92.1 96.8 Anomalous multiplicity 3.0 3.0 3.0 DelAnom correlation between half-sets 0.176 0.258 0.051 Mid-Slope of Anom Normal Probability 1.078 - - Average unit cell: 82.39 82.39 69.73 90.00 90.00 90.00 Space group: I 41 2 2 Average mosaicity: 0.10
