Could it be that for some reason (like the components of your solutions) you have Mg2+ in that site? Also, Magnesium is a common "contaminant", trace amounts are usually present in one chemical or another.
Subtle differences in the site might make it a "better" site for another lighter ion (we still do not fully understand the subtility of protein structures, and of their modifications). Fred. Fred. > Message du 30/06/10 03:36 > De : "xaravich ivan" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] Density changes from Positive to negative after ligand > addition and refinement > > Dear CCP4BB, > > I have come across something that might be pretty obvious to experienced > people but is making me crazy. > I have this great 1.15 angs data and I know that I have a Calcium ion (pics > attached) from previous structures of the same protein, that I have solved. > Rightly when I add waters with Arp solvent it does not put water at that > positive density. > Now whenever I have tried to put the calcium, and refine the structure it is > giving me a negative density at the metal site. I csn see that the 2fc-fo is > clear there, but why negative density. This is just the start of my > refinement and I have to refine multiple ligands in the structure and I > would like to get past this issue before that. > > I tried putting atom at the pointer, adding water and renaming it according > to the naming convention in the PDB for Calcium, but nothing. > > Your suggestions would be invaluable, as always. > > Ivan > > > [ Screen shot 2010-06-29 at 6.15.29 PM.png (375.3 Ko) ] > [ Screen shot 2010-06-29 at 6.21.22 PM.png (383.5 Ko) ]
