Dear Colleagues,
We are working on a structure where the density for a whole protein
chain (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3
Ang resolution). However, the initial difference density map and the
feature enhanced map (normal 2fo-fc map to a minor extend) support the
presence of this chain. Putting the chain seems equally wrong as not
putting it. Putting it reduces Rfree by 0.3%. As a conservative
researcher I feel tempted to deposit the structure without this highly
mobile/weakly occupied chain, but other researchers may say "he has
missed something". Handling this chain like a weakly occupied water is
probably wrong, but what is the optimal/correct way? Is there a general
opinion on how the escape this dilemma?
All the best,
Peer
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