I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and among the largest peaks in the difference map are small spherical blobs that seem to be attached (1.46 A here) to carboxylate O's (Figures). Are these likely artifacts? If not, how can I interpret/model them? One idea is that the acid has reacted with peroxide from the PEG to make the (hydro)peroxy-acid. I don't know how stable that would be, and I don't see any peroxyglutamate in Ligand Depot or HIC-Up. Another guess would be acid hydroxamate but I don't know how that would be generated. Methyl ester seems to be ruled out by the proximity of the two water molecules (2.45 and 2.48 A here) suggesting the mystery atom is an H-bond acceptor or donor. However since the occupancy seems to be < 1, the waters may be there only when the atom is not.
I guess another possibility is there is a lot of motion in the plane of the carboxylate (up and down here) which cannot be modeled by my isotropic B-factors. In some cases the green blobs appear on both sides of the carboxylate (but that could also be alternate conformations of peroxyglutamate).
The difference map (mFo-DFc, green) is contoured at 3 sigma (.06 e-/A^3). The difference peak is 5.4 sigma (0.1 e/A3).
The 2mFo-DFc map is contoured at 1.5 sigma (0.1 e/A3). 2mFo-DFc density extends to the difference peak if I contour down at 0.64 sigma (0.04 e/A3, third figure).
If I put an O atom there, link it with plenty of slack, and refine occupancy, it goes to 1.54 A from the carboxylate O and refines to occupancy 0.35, B-factor 15 (carboxylate O is 30). Now it is reached by 2mFo-DFc density at 1.5 sigma (0.1 e/A3).
Any suggestions would be welcome.
eab
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