As a general principle, I would always run MR searches in all 8 P2x2x2x space groups just to get some controls, if you haven't done it already. Trivial to do in Phaser
Phil On 8 Feb 2011, at 17:49, Francis E Reyes wrote: > Hi all > > I have a case of a dataset that indexed, integrated, and scaled well in P 21 > 21 21 (55.6410 81.6493 147.1294 90.0000 90.0000 90.0000) . The data > has an Mn(i/sd) of 2.1 at 3.5 A with a Rpim of about 0.398 at the highest > resolution shell (3.49-3.58). > > Analysis with phenix.xtriage warns of pseudotranslational symmetry (26% of > origin). > > > x y z height p-value(height) > ( 0.500, 0.000, 0.233 ) : 26.344 (2.681e-03) > ( 0.000, 0.338, 0.000 ) : 5.380 (8.476e-01) > > If the observed pseudo translationals are crystallographic > the following spacegroups and unit cells are possible: > > space group operator unit cell of reference setting > C 2 2 21 (b-1/4,c-1/4,2*a) x+1/2, y, z+1/4 (73.64, 55.47, 81.46, > 90.00, 90.00, 90.00) > > From what I've read about pseudo c-centering via pseudotranslational > symmetry, the problem exhibits itself with alternating weak and strong > reflections at low resolution, but become consistent at high resolution. > Inspection of the h+k parity groups via truncate does not show this behavior . > > Despite the fact the data was collected at the anomalous peak, I do not > observe any anomalous signal (DelAnom correlation between half-sets is 0.013 > for all data). > > Using a reasonably complete model (>80%) I searched for two molecules in the > ASU in space group P 21 21 21 and obtained a solution at TFZ=22.1 for two > molecules related solely by a translation. However the electron density maps > (after rigid body refinement) are not great (or maybe my expectations are too > high). I am encouraged by the fact the density is weak for a region of the > model which should have a different conformation, while strong density is > maintained for the rest of the molecule. > > Is this the proper way to approach pseudotranslation (i.e. is there any > reason to believe that the solution obtained by MR is not the correct > solution?). > > Is the space group determined? (i.e. does the pseudo c-centering affect > pointless's ability to analyze the systematic absences?). > > Is the lack of a pattern of alternating weak/strong reflections normal (would > observing this behavior be dependent on the crystal orientation) ? > > any advice would be greatly appreciated! (especially from those who have had > a case like this before) > > > F > > > --------------------------------------------- > Francis E. 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
