[ccp4bb] Translational pseudosymmetry?

[Owen Pornillos]

Dear ccp4bb –

I have questions with regards to crystal disorder that gives rise to  
translational pseudosymmetry.

We have a rotationally hexameric protein that crystallized in P3, with  
one hexamer in the asu.  The local 6-fold axis of the hexamer is non- 
crystallographic, and is essentially parallel to the crystallographic  
3-fold, which gave rise to translational pseudosymmetry.  Intensities  
for the (h,h+/-3n,l) reflections were on average about 8 times  
stronger than the weak reflections, and the native patterson gave an  
off-origin peak about 70-80% of origin (depending on the crystal) at  
fractional coordinates (2/3,1/3,0).  We are hypothesizing that the  
break in local 6-fold symmetry is caused by small rigid-body  
displacements of each subunit (as opposed to conformational changes in  
the protein), and we are trying to estimate the magnitude of the  
displacements in the crystal.

To do this, a perfectly symmetric hexamer with the local 6-fold axis  
parallel to the crystallographic 3-fold was generated, and then shifts  
were introduced to the atomic coordinates.  The direction of the shift  
was chosen randomly for each atom, and a single magnitude applied to  
all atoms, which was then changed incrementally.  Structure factors  
were calculated from these models, and their pattersons were  
examined.  The magnitude of the off-origin peak could be reproduced  
with an atomic shift of say, 1 Å.  Because all of these calculations  
were made with synthetic structure factors, this is not necessarily a  
reliable estimate.  The questions are, how far off are we, and in what  
direction (i.e., are these shifts underestimates or overestimates)?   
Is there a way to obtain a reliable estimate?

Thanks in advance,

Owen