Dear Yurong, I just wanted to check that you're using an up-to-date version of Phaser, which will account for the presence of translational NCS (tNCS). With older versions of Phaser, you could get apparent solutions that were incorrect but would give a high LLG just because they satisfied the tNCS. However, even with the current version of Phaser there's a potential problem here. Phaser will only take account of the tNCS if you're looking for an even number of copies (so that it can look for pairs related by the tNCS). I'm wondering if, in your case, the tNCS is generated in the model by placing the heterotetramer with its internal 2-fold parallel to the 2(1) screw axis along y. If that's the case, and you're only looking for one copy of the heterotetramer, then I'm afraid Phaser will ignore the tNCS. If indeed you're only looking for one copy of the heterotetramer, could you try looking for two copies of the half-tetramer instead (in the new version of Phaser)? That may give a clearer indication of the true symmetry and, if the solution is correct, the combination of translational symmetry and the screw axis should generate a full tetramer.
In cases like this, there's always a potential issue with twinning. I'd be interested in seeing the logfile (off-list) for the Phaser run, which should give an indication of whether the intensity moments suggest twinning, once the statistical effect of tNCS has been accounted for. Best wishes, Randy Read On 3 Dec 2012, at 11:49, Yurong Wen wrote: > Dear All, > Recently, I collected a dataset of a protein-DNA complex and indexed in > spacegroup P212121 to 3.4 Å. However, Phenix.Xtriage indicated the presence > of a very high pseudotranslational symmetry peak. I scaled the data in > spacegroup P222. When I used the protein heterotetramer as search model to do > the MR, solutions are suggested in P22121, P212121, P2212, P21212 and all > with a TFZ score higher than 15, LLG higher than 570. Then I used > phenix.refine to refine those solutions; however the Rfree is as high as > 0.54-0.56. The refinement strategy that I used for the refinement is rigid > body, group B-factors and XYZ coordinates. > > How to deal with this pseudotranslational symmetry problem? Does a solution > with such high TFZ scores mean that the correct one has been found? How to > solve the spacegroup problem in such situation? > > Do you have any suggestions? > > Thank you very much. > Greetings, > Yurong > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
