Dear Ed, What is the pH of your crystallization buffer? If it is acidic, either the azide or the carboxylate may be protonated. Also the local environment of the carboxylate can make a hugh difference in PKa. You could also use some Bayesian logic: given the elongated linear density, what else of the available components of your crystallization drop would fit?
Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edward A. Berry Gesendet: Sonntag, 7. Juli 2013 22:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] help identifying ligand In a structure I'm refining, there are a couple of oblong blobs associated with carboxylates. (screenshots at http://sb20.lbl.gov/berry/ccp4/azide/) If I modeled with two waters, they refine too close together for normal H-bond, 2.3 to 2.5 A; and their density is connected. I considered one water with alternate locations, but the distal position wouldn't make much sense if the proximal water wasn't there. The density is the right size for azide, which was present in the medium, but I expect a chemist would find it unreasonable to have anionic azide (pKa of hydrazoic acid ~4.6) associating with a carboxylate. Would that make sense? or does anyone have other suggestions? (resolution is 2.2A, contour 0.25 e/A^3 or about 1.3 sigma) Thanks, Ed
