Hi Satya Dev, You can feed the mtz output of SCALA to Phenix Xtriage and then see the presence of t-NCS and/or any other crystal pathologies. Another thing you can do is to merge and scale the data in P222 and then let the Phaser decide the best space group. Again, I am curious, when you ran pointless, did you check the absence conditions and the probability of assigning all the three screw axes?
Good luck! Sudipta. On Sat, Mar 18, 2017 at 5:42 AM, Eleanor Dodson <[email protected]> wrote: > You dont say whether there is Non cryst translation - that will be > reported at various stages - the pointless/aimless/ctruncate task gives it. > > But if it exists and the translation ihas a component of .5 along any > axis, that makes the SG estimate a bit uncertain - the absences could be > due to the NX translation. > > And even if the SG is correct - which likely after solving the MR with the > newest PHASER which tests carefully = then you will have zones with low > intensities, and those reflections always have a higher r factor of course. > > You could let Arp/Warp or Buccaneer rebuild starting from your existing > model? That is a verification that your solution is essentially right > > Eleanor > > > > On 18 March 2017 at 10:28, Isupov, Michail <[email protected]> wrote: > >> Hi, >> >> I have seen cases where in a correct space group >> 'R-work and R-free values 0.25 and 0.32 respectively' >> at 2 A resolution sound like not too bad values. >> In some of such cases when data from a different crystal >> in the same space group was available R-factors were much lower >> when the structure was refined against the new crystal data. >> I guess this phenomenon could be due to uneven freezing of the first >> crystal, >> or inconsistent degree of disorder between crystals. >> >> In other projects high R-factor values (e.g. FreeR around 33% at 2.1 A >> resolution) >> are consistent through a range of crystals >> even when the refinement is in P1, although the map quality is good enough >> to see cofactors and to build the missing parts of the structure (30% of >> residues). >> The disorder seems to be an intrinsic property of such crystal form. >> >> I do not know how to approach publishing these results since most >> referees will argue >> that such R-factors may be acceptable at 4A resolution but not close to 2 >> Angstrom. >> >> Best wishes, >> >> Misha Isupov >> ________________________________________ >> From: CCP4 bulletin board [[email protected]] on behalf of Randy >> Read [[email protected]] >> Sent: Saturday, March 18, 2017 9:29 AM >> To: [email protected] >> Subject: Re: [ccp4bb] No improvement in R-factor after Refmac. >> >> Hi, >> >> I was just going to make the same point! The only thing to add is that, >> if there really is translational NCS (which is certainly possible with 4 >> copies in the a.u.), then it’s essential both to account for it (which >> current versions of Phaser should do automatically, if you search for all 4 >> copies in one job) and to try all possible space groups. The situation >> Craig describes, in which it’s not immediately obvious whether your crystal >> has a crystallographic 2(1) and a pseudosymmetric non-crystallographic >> 2-fold or the reverse, is not uncommon. However, we’ve found that the >> likelihood score accounting for the effect of tNCS is pretty good at >> discriminating the two possibilities. >> >> Best wishes, >> >> Randy Read >> >> ----- >> 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: [email protected] >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> >> > On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <[email protected]> wrote: >> > >> > You really need to approach such situations with caution. Examination >> of the relatively small number of axial reflections probably show that >> there might be twofold screw axes in all three directions. But a >> non-crystallographic microscopic translation of nearly 0.5 in the direction >> of a crystallographic axis will give the same pattern of strong and weak >> reflections as a crystallographic twofold screw axis. If I were you, I >> would be very sure to try molecular replacement in all possible >> orthorhombic space groups. Several programs, including Phaser, will >> organize that exhaustive search across all eight possibilities for you. >> > >> >> On Mar 17, 2017, at 11:56 PM, Polisetty Satya Dev <[email protected]> >> wrote: >> >> >> >> Hi, >> >> >> >> We checked all possible space groups of orthorhombic crystal system >> using Scala and Pointless but the statistics show that P212121 is the >> possible space group. >> >> >> >> Thank You, >> >> Satya Dev >> >> >> >> On Fri, Mar 17, 2017 at 8:03 PM, Teplyakov, Alexey [JRDUS] < >> [email protected]> wrote: >> >> Check the space group. It may be orthorhombic with a pure rotational >> axis (e.g. P21212) or even monoclinic. >> >> >> >> >> >> >> >> From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of >> Polisetty Satya Dev >> >> Sent: Friday, March 17, 2017 9:51 AM >> >> To: [email protected] >> >> Subject: [EXTERNAL] [ccp4bb] No improvement in R-factor after Refmac. >> >> >> >> >> >> >> >> Dear all, >> >> >> >> I solved a structure at 2.0 A resolution with R-work and R-free values >> 0.25 and 0.32 respectively and I am stuck at Refmac step where there is no >> further reduction in R-factor. >> >> >> >> The above stated values were obtained after several rounds of manual >> refinement followed by refmac. There are also areas where electron density >> is missing around peptide backbone in one of the monomer in ASU. >> >> >> >> Can anyone please tell me how can I improve the electron density and >> R-factor. >> >> >> >> >> >> The structure solution was obtained using Phaser MR and here are the >> data statistics: >> >> >> >> >> >> >> >> Average unit cell: 81.95, 100.40, 156.96, 90.00, 90.00, 90.00, >> >> Space group: P212121, >> >> Completeness 99.5, >> >> Multiplicity 6.4, >> >> Four monomers per ASU. >> >> Solvent content: 47%. >> >> >> >> Thank you everyone, >> >> Satya Dev, >> >> JNCASR. >> >> >> > >> > >
