[phenixbb] pseudo-translational symmetry refinement

Arthur Glasfeld glasfeld at reed.edu
Wed Apr 30 20:59:00 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.

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.  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.

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

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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