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
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