I think REFMAC will generate anappropriate SSBOND entry in the pdb for
you if you run it from the GUI with Review restraintsoption
Eleanor
On 10/20/2010 08:40 PM, Seema Mittal wrote:
Hi All,
I have engineered intra-molecular disulfide bond in my protein monomer.
The protein functions as a homodimer.
In crystal structure, there is clean electron density for the S-S bond
in one monomer (bond length 2.2A), but there seems to be slightly messy
density for the same in the other monomer with (S-S bond length of
2.7A). An alternate conformation of one of the cys seems plausible on
the messy side. There is considerable negative density associated with
this region in both monomers, more so on the messy side.
My question is : do i need to select additional parameters or define any
sort of constraints during refinement, in order to refine this
introduced covalent bond?
Thanks much for your help.
Best
Seema Mittal
Graduate Research Assistant
Department of Biochemistry & Molecular Pharmacology,
970L Lazare Research Building,
University of Massachusetts Medical School,
364 Plantation Street,
Worcester, MA 01605
