Actually, the symmetry relating these solutions is a 2-fold around the y-axis, which is not a crystallographic operator in P41. So either this is a twinned crystal, and the two solutions relate to the two twin components, or the true symmetry is higher.
What is special about the solutions is that they indicate the starting model comes from an isomorphous or related crystal, because the operators correspond to rotations from the 422 point group and allowed origin shifts for P41. ----- 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 7 Nov 2012, at 17:34, Remy Loris wrote: > Dear Rui, > > If your search model is itself a homodimer, you expect to find 2 equivalent > solution > And indeed in your case: > > 50.3 + 128.6 = 178.3 (= aboput 180) > 0.2 + 179.8 = 180 > 219.8 - 38.7 = 181.1 (= about 180) > > indicating that both solutions are crystallographically equivalent. > > What does worry me is the apparent special position that you obtain for the > translation solution. Are you sure you do not have a higher symmetry or > cetered space group? > > Remy Loris > Vrije Universiteit Brussel and VIB > > On 07/11/12 17:39, rui wrote: >> Hi, Dear group, >> >> I recently collected a dataset about 2.5 A and integrated with P4. When I >> tried phaser I got a sol file looks like this, is this real solution? Is LLG >> high enough? >> >> SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9 >> SOLU SPAC P 41 >> SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 0.49916 >> -0.00408 BFAC -0.04000 >> SOLU ENSE ensemble1 VRMS 0.639 >> SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365 >> SOLU SPAC P 41 >> SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 0.49905 >> -0.00208 BFAC -0.06264 >> SOLU ENSE ensemble1 VRMS 0.642 >> >> Looks like there are two solutions,but in the output pdb file, I only see >> one solution (homo-tetramer). So I took this output pdb and run first round >> of refinement with Refmac, somehow, the structure fall apart if I use >> restraint refinement( lots of atoms are not connected any more ). If I use >> rigid body refinement, it's ok and Rfree is 52%. Does that mean the solution >> might not be correct? What's the acceptable Rfree for the initial >> refinement? Thanks a lot. >> >> Rui
