Occupancy.
On Sunday, 26 April 2020, 20:41:49 BST, Abhishek Anan
<rendezvous.a...@gmail.com> wrote:
Dear all,
Thanks for the suggestions. It is synthetic peptide so the residue
identity is unambiguous.
I am not clear on how to model both MET and SME in coot, do a real
space refinement and then save the file for refinement in phenix. I
tried alternate conformation and then mutating one of them but that
didn't work as both conformations were mutated. What I also just
noticed is that the refinement of structure with just SME results in
positive densities around all side chain carbons even with the SME.cif
loaded into phenix. What could be wrong here?
best wishes,
Abhishek
On 4/26/20, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
>
> 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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