On Jun 1, 2014, at 10:08 PM, Eze Chivi <ezech...@outlook.com.ar> wrote:
> Hello, when I refine my structure, I see negative density around the > disulfide bond. I have 7 copies per ASU, and I can see this density in many > of them. In some cases, I see positive density also (negative in the center > of the straight line linking S atoms, and positive in both sides). What can I > try to solve it? Is it due to radiation damage? Alternative conformation > (partial oxidation)? Incorrect disulfide geometry parameters? My resolution > is 2.1 A, R/Rfree are around 0.220/0.243, and similar results with refmac5, > phenix and PDBREDO. Please find two example pictures in attachment. > Thanks for your help! > > > Ezequiel > <disulfide.jpg><disulfide2.jpg> Dear Ezequiel: I apologize if I missed some crucial fact, but the simplest naive explanation would be the disulfide bonds became reduced somewhere along the line, since that would push the non-bonded sulfur atoms apart, relative to where you have them. You should be able to tell with a denaturing gel (run in the absence of DTT or equivalent). I’ve found a bit of Cu(II)-1,10-phenanthroline can help keep the disulfides oxidized. Try re-refining without the disulfide linkages, and see if the difference densities go away. Bill
