Dear Sudhir,
A blob surrounded by three Asp residues looks like a
positively charged ion. What else (buffer, additives) is in your crystallization
drop? I would also try to fit cysteine/serine. At 2 Å you will quickly see
whether or not this is correct.
Good luck!
Herman
Dear all,
I have a 2 A structure of an enzyme which show
12 molecules per asymmetric unit. While placing waters i found out some blobs
where i could not model any ligand. It is surrounded by 3 Asp molecules. I
have attached screenshot of the blob at 1.5 sigma cutoff 2fo-fc density.
Crystallization condition had following precipitants: PEG 1000, Peg 3350, MPD,
Ethylene glycol,and protein contained Glycerol. My protein is known to
bind Cysteine/Serine, though i haven't added any in crystallization buffer.
any suggestion what it might be are welcome. thanks in advance
--
best regards
Sudhir Kumar
Research Scholar
C/O
Dr. S. Gourinath
Structural Biology Laboratory
SLS, JNU,
New
Delhi-110067
