On 26/04/2020 16:21, Abhishek Anan wrote:
Dear all,
I have a peptide crystal structure at 0.97 Å that contains two surface
exposed Methionine. The CE atoms of both MET have a suspiciously high
b-factor >40 and a positive density. In addition, the sulfur atom SD
has a large negative density (b-factor ~23).
I initially suspected that the MET may have oxidized to MET-sulfoxide
and tried to model only the MET-sulfoxide. This again resulted in
negative density.
I think that the peptides might be partly oxidized which brings me to
my question. Is there a way to model both MET and MET-sulfoxide into
the density much like alternate conformation with options to refine
their respective occupancies.
Yes. This is called micro-heterogeneity
And is documented here:
https://www.wwpdb.org/documentation/procedure
That should "just work" if you then give the model to refmac.
FWIW, Coot is, AFAIR, not 100% happy with such models.
Paul.
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