As Aleks is suggesting, lower symmetry would be better. I had similar issues with one of my protein with unit cell dimensions 57, 57, 256. Xtriage suggested suggested three 2-fold merohedral twin operators (-h,-k,l; h,-h-k,-l; and –k,-h,-l). I went to lower symmetry (P31) and applied twinning law (-h,-k,l) during refinement and that reduced by R-factors. Pankaj
On Tue, Oct 4, 2016 at 10:22 AM, Aleksander Roszak < aleksander.ros...@glasgow.ac.uk> wrote: > Dear Rhys, > > I was not aware that twinning is not possible in P6322 however I agree > with Randy’s advise to check the lower symmetry P63 etc. > We were just collecting data which was apparently P6322 (according to > automated DLS processing: pointless) but the cell dimensions and our > knowledge of the protein composition was telling us that this SG is wrong. > Pointless/Aimless were however suggesting that twinning could be there and > lower symmetry could be an option. As Randy mentioned we used the unmerged > data which was luckily in P3 Laue group (original choice by EDNA and > probably XDS) to merge the data in P63. > That worked and we could then solve (and refine) the structure fine > however we had to apply the twinned refinement (in Refmac) to get the > reasonable R factors, R factors were much higher without the twinning. > This surely means that twinning is possible in P63 SG which then produces > data in over-symmetrical SG P6322. > > But try also Phaser with the option of the subgroups as Randy suggested, > it might work. > > Cheers, > Aleks > > > 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 > > -- Pankaj Kumar, PhD Gyanu Lemichhane lab <http://webhost.nts.jhu.edu/gl/> Centre for Tuberculosis Research Lab Department of Infectious Disease Johns Hopkins University School of Medicine 725 N. Wolfe St. Baltimore, MD 21205-2185 Lab phone: (410) 955-3967 pkuma...@jhmi.edu pkuma...@commsmail.johnshopkins.edu http://pankajimtech.webs.com
