Hmm - is the refinement complete? Maybe the GLU on the right could be moved to use some of that greenness? I try to make all sensible corrections, then check blobs.. Eleanor
On 3 July 2018 at 04:22, zaigham mahmood khan <mahmood.zaig...@gmail.com> wrote: > 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 > <https://maps.google.com/?q=1470+Madison+Avenue+New+York&entry=gmail&source=g> > New York > <https://maps.google.com/?q=1470+Madison+Avenue+New+York&entry=gmail&source=g> > > On Mon, Jul 2, 2018 at 10:23 PM, Uma Gabale <00000ebb5dcf3eaa-dmarc- > requ...@jiscmail.ac.uk> 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
