Yees - a translation of 0.5 along x means you must consider SGs P212121
and P2 21 21 since the absences will be present (at least at low
resolution) with either SG.
I dont know how good Phenix would be at distinguishing between z=0.233
and z=0.25
However even if the exact peak is at z0.25, it is nowhere near equal to
the origin peak, and pointless should be able to detect C centring
pretty accurately..
So I would consider the possibility of P2 21 21 , but be surprised if it
was a C /mmm symmetry..
On 02/08/2011 05:49 PM, 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
