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!
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 Kadirvelraj
> Biochemistry and Molecular Biology
> 120, Green Street
> University of Georgia
> Athens, GA 30605
> Tel: (706) 583 0303 <(706)%20583-0303>
> 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