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Andrew Wong wrote:
In structures that have obvious hydrophobic cores/regions, that have stray non-continous density, what do ppl usually try to put in there? Of course if there're things like glycerol, co-factor in the condition, you can try those. But what if the condition has nothing else except the common buffers and fairly large MW PEG?
Symmetrical diatomic molecules like N2 and O2 are quite nonpolar, and significantly more soluble in oils than in water. They don't seem to occur much in the PDB, but is that because there is a specific reason they wouldn't be visualized? or people just haven't considered them? N2 at least is a universal component in protein crystallization setups, I should think, and it is a lot of trouble to exclude oxygen. If you really don't know what it is, it might be better to consider the ligand UNL (present in many forms in HIC-Up but not in Ligand-Depot - I hope the PDB still allows it. That would alert the end users that there is something interesting but unidentified here, rather than tricking them into believing it is a water or an oxygen. Make sure the ATOM name doesn't start with U (OUK, CUK, NUK are ok) or some validation programs will see it as uranium. Ed
