Dear Rhys, There's one important consideration to start from, which is that the space groups P6322 and C2221 with their associated cell dimensions are two different ways to describe the shapes of the unit cells and the positions of the spots. You can see this by running phenix.explore_metric_symmetry on the two cases. (Perhaps there's a tool in CCP4 for this as well?) So dehydrating your crystal hasn't really changed the cell, and the underlying symmetry will be basically the same (give or take the possibility that a symmetry operator that is crystallographic in one case might be pseudosymmetry in the other, if things move a bit in the crystal).
As you say, there are no twin operators for P6322 so, if that crystal is twinned, this implies that the true symmetry is lower and that part of the apparent symmetry arises from the twinning. You don't mention anything about how well the data merge in P6322 for the first data set, but it is also possible to computationally twin your data by merging in too high symmetry! Have you run pointless on the unmerged data from both crystals? That may give you a better idea of the actual symmetry of the diffraction pattern (part of which may come from twinning). If the two data sets give different results, then maybe the true symmetry is closer to the lower symmetry you see from the two data sets. Do you have a molecular replacement model? If you do, then molecular replacement in lower symmetry subgroups can work very well to discover the true symmetry while solving the structure at the same time. Phaser has some nice new features to list the possible subgroups and to expand the data to lower symmetry (though the latest version, which is available in Phenix nightly builds but not quite yet in CCP4 works considerably better than the current CCP4 version). Also, the tool Zanuda in CCP4 can be very effective for working out the true symmetry. Best wishes, Randy Read > On 4 Oct 2016, at 00:26, Rhys Grinter <rhys.grin...@monash.edu> wrote: > > Dear All, > > As I have approached my crystallography from a biological perspective, > sometimes so of the more mathematical/geometrical aspects sometimes perplex > me. I was wondering if anyone would be able to clarify what is going on with > some problematic crystals I'm working on. > > I've grown crystals of a protein which forms a concentration dependent > oligomer. This is almost certainly a physiological oligomer and probably is a > hexamer at maximum oligomerisation (although maybe a trimer). These crystals > diffract poorly, however after some optimisation I managed to collect data to > around 3.6 A, with a predicted space group of P6322 with unit cell dimensions > of 177, 177, 150 . In order to improve diffraction I performed dehydration on > these crystals. This seemed to improve diffraction to around 3A (although as > the crystals are quite variable attribution of effect is a little difficult), > however the best space group I can find for indexing is C2221 with a unit > cell of 177, 310, 151, XDS doesn't process the data when I force the previous > P6322 SG. It seems also that the C2221 space group isn't the correct choice > as the merging stats are worse than I would expect from looking at the > diffraction pattern. > > Additionally, the intensity statistics from both space groups suggests > twinning. Although for the P6322 space group it says twinning is not > possible. If this is the case what is causing these abnormal intensities and > is this related to my SG ambiguity? > > Also what is the best what to proceed with processing in this case? > > Cheers, > > Rhys > > -- > Dr Rhys Grinter > Sir Henry Wellcome Fellow > Monash University > +61 (0)3 9902 9213 > +61 (0)403 896 767 ------ 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
