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.it>wrote: > 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
