Uma, that is not something that we see regularly in the crystal structures. But i never used PFPE either. So, you may try PFPE. If this is not PFPE, then you may read the biology of the protein.
Also I can see green density, but these green blobs are devoid of blue density. So i will be cautious. May be just add water molecule in each blob, and re-run refinement. You will see a change in color of the blobs, that may indicate something.. If red blobs appear around the water molecules, i will consider it just a noise. Alternatively, you will see green density connecting the water molecules... Best wishes -Z Zaigham Mahmood Khan, PhD Icahn School of Medicine at Mount Sinai Department of Oncological Sciences 1470 Madison Avenue New York On Mon, Jul 2, 2018 at 10:23 PM, Uma Gabale < [email protected]> wrote: > Dear all, > > We came across a blob of unidentified electron density in a shallow cavity of > a bacterial protein structure (pictures attached). It is surrounded by > residues Asp, Arg, Gln, His, Glu, Thr, and Trp. > > The protein was expressed in *E. coli* BL21(DE3) and purified on Ni-NTA > followed by gel filtration. The purification buffers included Tris, > crystallization condition had HEPES and PEG3350; perfluoropolyether was > used as a cryoprotectant. > > We would appreciate any help in identifying it. > > Thanks and regards, > > Uma. > -- > Uma Gabale, PhD > Research Associate > Molecular and Cellular Biochemistry > Indiana University Bloomington > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
