Inevitably Rfactors are higher for data sets with strong pseudo translation . It forces a sub set of the reflections to be systematically weak and weak reflections always have higher R factors.. So if your maps look good I think you can be happy with your results.
As Randy says quite often false "twinning" is detected when the data is processed with too low symmetry.. The L test is prett reliable - if it says - no twinning I would believe it! Eleanor On 2 February 2018 at 16:28, Randy Read <rj...@cam.ac.uk> wrote: > Dear Renu, > > If the intensity statistics (especially the L-test and Phaser's second > moments tests after the tNCS correction) do not indicate twinning, then you > probably would not be justified in assuming that the crystal is twinned, > unless you find good evidence (e.g. from the symmetry of the MR solution in > P1) that the crystal is pseudo-symmetric rather than exactly P21. > > I think if you look closely at the xtriage output, you should find > provisos warning you that the results from the tests using potential twin > laws can indicate twinning when, in fact, the data are simpy merged in too > low symmetry. The tests using potential twin laws are based on the > assumption that twin-related reflections should have independent > intensities, which is not true *either* when there is twinning *or* when > the data have been merged in too low symmetry and the reflections really > are related by symmetry. > > Best wishes, > > Randy Read > > On 2 Feb 2018, at 15:27, Renuka Kadirvelraj <r...@ccrc.uga.edu> wrote: > > Dear All, > > I am trying to refine a 1.9 A structure that indexed with excellent > statistics (*XDS*) into a primitive monoclinic cell with cell lengths > a=81.33, b=90.11, c=113.25 and beta angle =102.15. Data analysis ( > *Xtriage*) indicated strong pseudo-symmetry with an off-origin peak (53% > of origin peak) at fractional coordinates (0.07, 0.5, 0.19). The intensity > statistics did not indicate twinning and *Pointless* picked P2(1) as the > space group with a 94% probability. Molecular replacement (*Phaser*) gave > a solution with 4 molecules in the asymmetric unit with appropriate packing > of symmetry-related molecules and NCS-restrained refinements with TLS led > to very good quality maps. However, the Rfree for the completed model has > stalled at 28% (Rwork is at 24%). > > I could not solve the structure in P2. Data processed in P1 has almost the > same dimensions as the monoclinic cell (a=81.37, b=90.14, c=113.29) and MR > with *Phaser* located 8 molecules in the asymmetric unit. The data scaled > in P1 also has translational pseudo-symmetry at (0.06, 0.5, 0.185). Intensity > statistics do not indicate twinning but *Xtriage* detects the two-fold as > a pseudo-merohedral twin (-h,k,-l) andsuggests the likely point group is > P2. Initial refinement indicates the Rfree will likely remain high for the > structure in P1 as well (Rfree ~37% and Rwork at 34%). > > I would really appreciate advice regarding the stalled Rfree and finding > the true space group. > > Many thanks, > Renu > > > --------------------------------------------- > Renu Kadirvelraj > Biochemistry and Molecular Biology > 120, Green Street > University of Georgia > Athens, GA 30605 > Tel: (706) 583 0303 <(706)%20583-0303> > r...@ccrc.uga.edu > > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > <+44%201223%20336500> > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > <+44%201223%20336827> > Hills Road E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >
