---------- Forwarded message ---------- From: Polisetty Satya Dev <pvss...@gmail.com> Date: Mon, Mar 20, 2017 at 1:35 PM Subject: Re: [ccp4bb] No improvement in R-factor after Refmac. To: Sudipta Bhattacharyya <sudiptabhattacharyya.iit...@gmail.com>
Hi, I had tried running xtriage but it does not show any sign of NCS. But pointles is showing the following warning * "one or more zones have data systematically missing from the input file thus we cannot determine if reflections are truly systematically absent"* Thank You, Satya Dev On Sun, Mar 19, 2017 at 5:22 AM, Sudipta Bhattacharyya < sudiptabhattacharyya.iit...@gmail.com> wrote: > 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 <eleanor.dod...@york.ac.uk > > 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 <m.isu...@exeter.ac.uk> 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy >>> Read [rj...@cam.ac.uk] >>> Sent: Saturday, March 18, 2017 9:29 AM >>> To: CCP4BB@JISCMAIL.AC.UK >>> 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: rj...@cam.ac.uk >>> Cambridge CB2 0XY, U.K. >>> www-structmed.cimr.cam.ac.uk >>> >>> > On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <cabing...@wisc.edu> 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 <pvss...@gmail.com> >>> 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] < >>> atepl...@its.jnj.com> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf >>> Of Polisetty Satya Dev >>> >> Sent: Friday, March 17, 2017 9:51 AM >>> >> To: CCP4BB@JISCMAIL.AC.UK >>> >> 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. >>> >> >>> > >>> >> >> >
