Hi Uma, It is risky to guess based on one-view of of the density from 2-dimensional images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!! If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it be an alternate conformation of the Arg side-chain. One could build, and re-refine and see if negative mFo-DFc features shows up.
Hope this helps, Partha On Tue, Jan 24, 2017 at 12:19 PM, Uma Gabale < 00000ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > While refining a structure at 2.5 A resolution, we observed a > semi-circular/crescent shaped electron density blob as shown in the > attached picture. We have been unable to identify it so far, and would > appreciate any help in identification. > The protein was expressed in *E. coli* BL21(DE3), purified on Ni-NTA > followed by gel filtration. The purification buffers included Tris and NaCl > (no detergent/ other ingredients except for imidazole for Ni-NTA). > Crystallization condition had HEPES and PEG3350; no cryoprotectant was used. > The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe. > Thanks and regards, > Uma. > > -- > Uma Gabale, PhD > Research Associate > Molecular and Cellular Biochemistry > Indiana University Bloomington >
