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Hi Francis, I would consider the possibility of a orthorhombic sg (a~b with twinning). If unlucky maybe even monoclinic. Cheers Roberto On 5 Feb 2009, at 18:10, Francis E Reyes <[log in to unmask]> wrote: > It seems like this space group will be the death of me. > > I'm working on a structure in SG P41212 one molecule per asu that was > solved with experimental SAD phases. The resolution is to 2.5 and the > refinement is stuck at an R/Rfree of 30 and 33 with bonds rmsd of > 0.011 and angles of 1.597 . The unit cell is 73.604 73.604 114.279 > 90.00 90.00 90.00. > > I'm considering the case of perfect twinning where the real s.g. is > P41 masked under the higher symmetry in P41212. > > It seems to be the case in perfect twinning that the approach is to > molecular replace the refined model into the lower space group. I > reindexed my data to the lower space group P41 and molecular replaced > into the reindexed data with Phaser. A single was solution was found > with 2 mol per asu (39.6% solvent content) related by NCS. > I've refined the now two fold ncs related structure in P41 to a much > more respectable R/Rfree of 25.2 and 28.6 with rmsd bonds at 0.004 and > angles at 0.865 refining with a twin law and NCS as implemented by > phenix.refine. > > However I'm not happy: > [1] a simmulated anneal omit map one of the monomers in P41 where 5 > residues in a non crystal contact region of the molecule (I wanted to > challenge the omit map) shows nearly no density. (the SA OMIT map was > generated with phenix.autobuild using the same refine parameters as > the final round of refinement) > [2] the NCS selection is a little bit troubling. (maybe the phenix > developers can chime in on this) > reference = chain 'B' and (resseq 243:293 or resseq 310:370 ) > selection = chain 'A' and (resseq 243:293 or resseq 310:370 ) > seems as if resseq 243:293 is behaving differently than 310:370? > [3] the densities of the side chains of a helix (not an xtal contact) > are poorly defined, with geometry for the backbone not so good. > > > There's talk about choosing the correct MR solution (see On the > molecular-replacement problem in the presence of merohedral twinning: > structure of the N-terminal half-molecule of human lactoferrinW. A. > Breyer, R. L. Kingston, B. F. Anderson and E. N. Baker ) . I use > phaser to pick my MR solution for P41. Could phaser possibly have > chosen poorly? > > Thanks! > > FR > > > --------------------------------------------- > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D