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
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