Dear All,
I have 2.6 A data and unambiguous molecular replacement solution
for two copies/asymmetric unit of a 80 K protein for a crystal integrated
in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9.
Refinement allowed rebuilding/completion of the model in the noraml way
but the R-free does not go below 30%. The map in the model regions looks
generally fine but there is a lot
of extra positive density in the solvent regions (some of it looking
like weak density for helices and strands) and unexpected positive
peaks within the model region.
Careful inspection allowed manual positioning of a completely different,
overlapping solution for the dimer which fits the extra density perfectly.
The two incompatible solutions are related by a 2-fold axis parallel to a.
This clearly suggests some kind of twinning. However twinning analysis
programmes (e.g. Phenix-Xtriage), while suggesting the potentiality
of pseudo-merohedral twinning (-h, l, k) do not reveal
any significant twinning fraction and proclaim the data likely to be
untwinned. (NB. The programmes do however highlight a
non-crystallographic translation and there are systematic intensity
differences in the data). Refinement, including this twinning law made
no difference
since the estimated twinning fraction was 0.02. Yet the extra density is
clearly there and I know exactly the real-space transformation between
the two packing solutions.
How can I best take into account this alternative solution (occupancy
seems to be around 20-30%) in the refinement ?
thanks for your suggestions
Stephen
--
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Dr. Stephen Cusack,
Head of Grenoble Outstation of EMBL
Group leader in structural biology of protein-RNA complexes and viral proteins
Joint appointment in EMBL Genome Biology Programme
Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell
Interactions (UVHCI)
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Email: [email protected]
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