[phenixbb] pseudo-translational symmetry refinement

Peter Zwart PHZwart at lbl.gov
Wed Apr 30 21:23:43 PDT 2008

> I hope it's OK if I chime in with this problem as well.  I am working
>  with a site-directed mutant of a commonly studied protein in our
>  lab.  It crystallize in P3121 and its unit cell is doubled along the
>  c axis relative to a unit cell (P3221) that we have commonly seen
>  with other mutants (the edges are roughly 55 x 55 x 88 or 55 x 55 x
>  176).  Xtriage also picked up the pseuotranslational symmetry (0, 0,
>  0.5), which is not surprising given the unit cell dimensions.

If you are jusing the latest version (of of the lastes) it should
actually tell you what the unit cell would be if the pseudo
trans;lation would be a true crystallographic translation.

>  I was aware of the problem with weak and strong reflectiions, but
>  that is not so obvious in our case.  In HKLview one can see that in
>  layers perpendicular to the c* axis, strong and weak reflections
>  alternate out to about 8 Å, but the rest of the data (to 2.6 Å)
>  appears - at least visibly - to be roughly consistent in intensity.
>  Certainly when looking at the h0l or 0kl planes, there isn't any
>  obvious alternation at higher resolution.

If the differences are subtle / relatively minor, this is what is to
be expected (watch out, a lot of hand waving):  at low resolution, the
symmetry does not "appear to broken" resulting in strong modulations
as if it were crystallographic symmetry. AT high resolution,
deviations from ideality are so large that modulations are not so
obvious anymore.

What is the size of your off origin patterson peak as computed by xtriage?

> We quickly obtained a
>  model by molecular replacement but have stalled in refinement at an R/
>  Rfree of 30/38 (we have not tried TLS yet).  The most obvious
>  difficulty with the model is seen using density fit analysis in coot
>  - one domain of one of the subunits in the asymmetric unit (related
>  by translation NCS to the other) has weak density.

try TLS, it might help.

>  Maybe this is just the luck of the draw - a crystal whose contents
>  include 50% well ordered subunits and 50% not well ordered, but I'm
>  curious if there is something obvious we should be trying.

Not sure. 50% ordered and 50% not ordered sounds a lot like order
disorder twins (OD). I am not sure what canb by done with that type of
data in terms of refinement.

>  By the
>  way, xtriage found no evidence of twinning, and the data also passed
>  muster with dataman (Padilla-Yeates) and Todd Yeates' server.

Xtriage does use the Padilla Yeates test as the primairy vehicle for
twin detemination, combined with the presence of twin laws of course.

Beware that the presence of a full complement of nightmares such as OD
twinning, merohedral twinning, pseudo symmetry etc etc can make
intensity statistics look like all is fine.


>  Thanks in advance,
>  Arthur Glasfeld
>  Department of Chemistry
>  Reed College
>  P.S.  If anyone is interested I can send a figure with the hklview
>  layers perpendicular to c* (hk0, hk1, hk2, hk3, hk4, hk5)
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
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