Bart Hazes wrote a program (and published as well, Hazes & Dijkstra perhaps) called SSBOND I think. I cannot remember exactly what the computer program does, but it certainly has a data base of "possible" disulphide bond conformers. Hence I would myself certainly check your second didulphide to see if one of these conformers would explain the density better. As long as the model is not into its proper conformation (or conformations if there are several) then the density will not be optimal. There may be SS bond conformer libraries in graphics programs, I do not know (never needed that myself).
Fred. > Message du 20/10/10 21:41 > De : "Seema Mittal" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] refining structures with engineered disulfide bonds > > 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. > > BestSeema MittalGraduate Research AssistantDepartment of Biochemistry & > Molecular Pharmacology, > 970L Lazare Research Building, > University of Massachusetts Medical School, > 364 Plantation Street, > Worcester, MA 01605
