Hi -
At higher resolution like you have, it seems common to me to detect
alternate conformations for the larger solvent molecules, making it more
difficult to decide at first glance what occupies the density. After you
put in something, the new difference peaks should tell you if there is
another conformation, which, may not occupy the same overall space, that
may need to be added. There will be water shifts due to this too. These
cases are easier to spot if the protein also has alternate conformations
adjacent to the blob in question. Data near 1 angstrom can be a lot of work.
D
On Thu, Dec 12, 2013 at 4:17 AM, Danilo Belviso danilo.belv...@ic.cnr.itwrote:
Dear Afshan,
Maybe what I suggest you have already tried: have you tried to fit a
citrate molecule? The blob seems to be branched, thus compatible with such
organic molecule.
Danilo
On Thu, 12 Dec 2013 03:34:07 -0800, Afshan Begum afshan...@yahoo.com
wrote:
Dear Experts,
I collected a data set (1.12A) of one of my target proteins, and built
a model by molecular replacement.
I then exam the model by Coot and found one unidentified blob. I am
unable to to identified a blob which appeared on the surface of the
molecule
its close to residues 115 SER
the protein purified in 10 mM Na-phosphate buffer, 100mM KCl and
crystallized in 1.6 M sodium citrate, 3.5% _v/v _glycerol
I have attached the picture of the blob.
I would be thankful for your kind suggestions.
Best Regards
AFSHAN
--
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA
