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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