I disagree with Nat—it is more likely that the blob is a chloride than a water, and dramatically more likely than a “nothing.” And it’s certainly not “wildly speculative,” considering that there is 200 mM Cl- in the crystallization cocktail, and the type of contacts it makes. Not sure why there is this level of suspicion about the poor halide when waters generally get assigned so haphazardly. I would say that there are probably more “wrong” waters in the PDB than wrong chlorides, but there’s not much fuss about that. I suspect that whatever reason you will give for not fussing about waters, you can apply that reason to chloride as well. I would concede that if some conclusion will be reached based on its being a chloride, one should be especially rigorous, (this would be true for water as well) but otherwise cannot see any reason for being so particular. If it fits the data best and is plausible, I say go for Cl-.
Hopefully your reviewers will at least agree with each other! JPK From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Nat Echols Sent: Wednesday, January 21, 2015 11:35 AM To: [email protected] Subject: Re: [ccp4bb] chloride or water On Wed, Jan 21, 2015 at 12:16 AM, Engin Özkan <[email protected]<mailto:[email protected]>> wrote: Carbon in chloride's coordination sphere? To me, it looks like you have serious vdW violations, and neither water nor chloride could go there. Halides can interact with carbon too - discussed in Dauter & Dauter (2001) - although I think this is more common with iodide than chloride. But this instance is totally unconvincing without anomalous data. It would be better to leave it entirely empty than to put in something wildly speculative - there are far too many spurious chlorides in the PDB already, which of course makes it even more difficult to come up with general rules about binding patterns. -Nat
