Dear Hauke, others pointed out that there is little suspicious about your data, and you can probably continue refining in P21. You also have a reasonably large unit cell, so stick to the defaults regarding Rfree selection.
4.5A resolution is just quite hard to work with, but otherwise I don't think there is anything problematic about your data. Best regards, Tim On Monday, October 31, 2016 09:44:35 AM Hillen, Hauke wrote: > Dear Tim, > > In this case, I was using my anomalous dataset truncated at 5A resolution > for refinement and used Phenix to generate a Free R array: > > Number of work/free reflections by resolution: > work free %free > bin 1: 49.6881 - 10.7634 [4605/4610] 4403 202 4.4% > bin 2: 10.7634 - 8.5575 [4565/4568] 4365 200 4.4% > bin 3: 8.5575 - 7.4799 [4588/4591] 4389 199 4.3% > bin 4: 7.4799 - 6.7979 [4592/4597] 4394 198 4.3% > bin 5: 6.7979 - 6.3117 [4616/4619] 4415 201 4.4% > bin 6: 6.3117 - 5.9402 [4582/4587] 4386 196 4.3% > bin 7: 5.9402 - 5.6431 [4589/4594] 4388 201 4.4% > bin 8: 5.6431 - 5.3978 [4567/4570] 4367 200 4.4% > bin 9: 5.3978 - 5.1902 [4572/4577] 4372 200 4.4% > bin 10: 5.1902 - 5.0113 [4621/4627] 4420 201 4.3% > overall 43899 1998 4.4% > > I assume that if there is really twinning, one should choose rather more > reflections than less for the free R array to have around 5% for each twin > fraction? > > Kind regards, > Hauke > > > ------------------------------------------------------- > Hauke Hillen > Department of Molecular Biology > Prof. Dr. Patrick Cramer > Max-Planck-Institute for Biophysical Chemistry > Am Fassberg 11 > D-37077 Göttingen > Germany > > E-Mail: hauke.hil...@mpibpc.mpg.de<mailto:hauke.hil...@mpibpc.mpg.de> > Phone: +49-551-201-2864 > > > > > > On Oct 28, 2016, at 4:03 PM, Tim Gruene > <tim.gru...@psi.ch<mailto:tim.gru...@psi.ch>> wrote: > > Dear Hauke, > > when you use twin refinement, your R-factor is bound to drop whether it is > twinned or not. In your case Rfree rises, which is actually hinting at your > data not being twinned. How many reflections do you have in the Rfree set? > > Best, > Tim > > On Friday, October 28, 2016 1:59:29 PM CEST Hillen, Hauke wrote: > Dear Kay, > > Thank you for your answer! > I have meanwhile processed my anomalous data also also as P1 and solved the > structure with MR-SAD in P1, which works flawlessly and gives the same > solution. Compared to P21, I now have 4 instead of 2 molecules in the ASU, > which makes sense. I then tried refinement in P1 with or without applying a > twin law in phenix.refine. The result seems very clear. Without twin law, > R/Rfree after one round of rigid body refinement drop to 34/38. With twin > refinement, the same refinement results in R/Rfree of 29/42. My current > suspicion is therefore that my data are truly P1, with an NCS axis parallel > to a crystallographic axis (suggested by Xtriage). Could this > pseudosymmetry lead XDS to falsely identify my data as P2 instead of P1? > > Best wishes, > Hauke > > > ------------------------------------------------------- > Hauke Hillen > Department of Molecular Biology > Prof. Dr. Patrick Cramer > Max-Planck-Institute for Biophysical Chemistry > Am Fassberg 11 > D-37077 Göttingen > Germany > > E-Mail: > hauke.hil...@mpibpc.mpg.de<mailto:hauke.hil...@mpibpc.mpg.de><mailto:hauke. > hil...@mpibpc.mpg.de> Phone: +49-551-201-2864 > > > > > > On Oct 28, 2016, at 3:51 PM, Kay Diederichs > <kay.diederi...@uni-konstanz.de<mailto:kay.diederi...@uni-konstanz.de><mailt > o:kay.diederi...@uni-konstanz.de>> wrote: > > Dear Hauke, > > the conversion of intensities to amplitudes is an area with unsatisfactory > solutions, and the approaches of (and the assumptions made by) the > different programs differ. Low-resolution data are often anisotropic, which > adds difficulties. You could try CCP4 truncate/ctruncate and > GlobalPhasing's staraniso. The latter in particular should treat > anisotropic diffraction more properly. Probably you get yet other answers > from xtriage when fed with those amplitudes. Possibly this will add to the > confusion, but I'm not sure it is worth worrying about this too much. > > Having said that, it seems to me like the primary and most unspoiled data > are the intensities. I don't see anything suspicious in the > xtriage-on-intensities output that you posted. > > good luck with your difficult project! > > Kay > > > -- > -- > Paul Scherrer Institute > Dr. Tim Gruene > - persoenlich - > OFLC/102 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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