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. > >> > > >
