I believe you could try treating this Asp residue as an unnatural amino acid (FAD-Asp), and refine your structure with it.
Peter > Date: Thu, 10 Sep 2009 15:27:58 +0100 > From: kpodzelin...@gmail.com > Subject: [ccp4bb] Refinement of covalent ligand in Refmac5 > To: CCP4BB@JISCMAIL.AC.UK > > Hello! > > I have an FAD cofactor that appears to be covalently bound to the Asp side > chain (~1.6 A away). I was told that I need to refine the structure after > indicating the covalent linkage in the pdb. > > If I add a line in the pdb "LINK #### ####" and then refine in Refmac5, FAD > gets all messed up and shifted out of its density and R factors go up by ~5%. > > Any suggestions on how to do this refinement would be greatly appreciated! > > Kateryna _________________________________________________________________ Click less, chat more: Messenger on MSN.ca http://go.microsoft.com/?linkid=9677404
