Dear all, I agree with MM about the ligand and complex structures. Even in the most honest circumstances, it is easy to get carried away with hopes and excitement. My personal embarassing experience was some years ago. It involved a protein that I had crystallized in a different space group in the presence of inhibitor- 2.5A data. The MR model had some gaps a moderate distance from the binding pocket. Lo and behold, some new, very rough density appeared very very close to a binding site- close enough to get my hopes up. I communicated my elation to the PI, handed over pictures of the rough blobs of density, and started trying to build the ligand in.
I should have moderated my emotions in light of the early state of the refinement. After finding a somewhat plausible fit in the density, I ran several rounds of the Wonderful Amazing Revealer of Proteindensity program. By the end I was almost in tears. The difference density began to take on a helical shape, and then the connections started growing, leading all the way up to one of the gaps. Side chains too, so I had no trouble with the register. The R-factors didn't change too much, but the geometries and maps in the area started looking really nice. Or should I say, proper. Very nice silver platter (that my head was on when it was handed it back to me). Lisa
