Do you mean main chain carbonyl oxygen?
Side chain carboxyl oxygens can suffer decarboxylation during data
collection.
The C-terminal residue will have a carboxylate group subject to the
same decarboxylation. My guess is that you mean a C-terminal residue.
James
On Mar 7, 2009, at 4:11 PM, john peter wrote:
> Hi All,
>
> Sorry if this is a trivial question. I'm refining my first structure
> at 2.1 A resolution. There is no density for the main chain carboxyl
> oxygen of a residue even at 0.5 sigma level in 2FoFc map. The FoFc
> map shows a negative density when I place the oxygen, satisfying the
> standard geometry condition. Could someone tell me what to do in this
> situation. Should I make the occupancy of the oxygen zero. Any
> comments would be gratefully appreciated.
>
> Thanks very much.
>
> John Peter
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