Try refining without disulfide bond - from the way density looks it might work. Whether this is what happens in vivo is a different question entirely.
Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Eze Chivi <ezech...@outlook.com.ar> </div><div>Date:06/02/2014 1:08 AM (GMT-05:00) </div><div>To: CCP4BB@JISCMAIL.AC.UK </div><div>Subject: [ccp4bb] negative density around disulfide bond </div><div> </div>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
