Hi, since several people mentioned R factors in this conversation I thought I remind that R-factors are not comparable between refinements using twinning and not. For example, R-factor decrease after switching to twin refinement doesn't mean much; you can't use R factor drop as an argument for considering twining vs not considering it at all!
Pavel On Tue, Oct 4, 2016 at 7:43 AM, Pankaj Chauhan <pankajimt...@gmail.com> wrote: > 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 > >
