Dear Peer,
This is indeed a very strange situation. If you have a molecule sitting
on a crystallographic 2-fold, it would almost certainly overlap with its
symmetry-related copy. A more exotic solution would be a 2-fold disorder
around the axis, with each chain having a 50% occupancy, but I have
never heard of such a thing with a protein.
Did you check whether your dataset is twinned?
Regards,
Pedro
On 26/08/2021 10:54, Peer Mittl wrote:
Der CCP4 community,
Is there a refinement program that can handle protein monomers sitting
on crystallographic 2-folds?
This is probably a strange question but we have the following
situation. We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6)
and a clear molrep solution with 2 chains, albeit with tNCS (0/0/0.5)
that can be refined to around 27/33% Rfactor. According to Vm a third
chain could be present. So far so good, but there is clear difference
ED for a third chain sitting exactly on the 2-fold. Since the protein
has a peculiar shape, one can tell even its orientation. I can relax
the symmetry to P32 (or even P1) and place the missing chain with 50%
occupancy on the 2-fold. This model can be refined, but I do not like
this work around, because the data is clearly P3221.
Any hints on similar crystal pathologies and how they have been
handled would be helpful.
All the best,
Peer
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