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
