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[ccp4bb]: Ghost Cysteine!
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Sorry this question is not directly related to CCP4 but may be
encountered by someone used CCP4.
A three-atom group (3 atoms arranged one by one, without branch)
was found to attach to the sulfur atom of an active-centered
cysteine in a very pretty electron density map, which might mean
a modified cysteine. During protein expression and crystallization,
2-mercaptoethanol used to be taken to protect the cystiene. However,
1) The electron density around the "modified cysteine" looks as:
(Cys)Ca-Cb-S-A1-A2-A3 . (A1-A3 are appended atoms)
If A1-A2-A3 represent S-C-C of the 2-mercaptoethanol, then
it means its O atom is not viewable, it is a little hard to accept
since the pretty low B-factor of A1-A2-A3, say 15-20.
2) After exchanging with the 2-mercaptoethanol-free buffer [5 times,
every time 1-day used for reaction equilibrium, and buffer volume
Old:New=1:10], crystallization was performed and succeeded,
but the extended electron density could be "erased".
So, I would like to hear some other suggestions. It will also be
appreciated if you suggest me some literatures about non-standard