Just to add to Phil and Eleanor's response...
I would NOT use Phaser for MR with PTS present. It doesn't handle it
correctly yet, since the likelihood targets don't account for PTS.
Others may be able to explain it better.
Its probably not C-centered (as Eleanor mentions) and you should try the
other primitive cell options.
From what I understand about seeing (or not) the strong/weak reflection
behavior... it is proportional to the size of your off-origin Patterson
peak so it is more difficult to see when the off-origin peak is small
(26% in your case). Crystal orientation, I guess, could also be a reason
for not visualizing it on the diffraction image, but it still should be
apparent in the stats since Xtriage found it.
If it was me... If your off-origin peak was over 50% of the origin peak
height AND after inspecting the Patterson map to see if it lies at
z0.25, then you MIGHT be able to solve and refine the structure in
C-centered orthorhombic cell. The advantage of this would be that you
wouldn't be refining against a large portion of weak reflection data. In
your case, however, since your weak reflections are not really that weak
you shouldn't have too much of a problem refining.
Hope this helps.
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email: schue...@anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687
On 02/08/2011 11:49 AM, 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
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8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
