It looks like structured PEG to me. Did you have PEG as a precipitant in you crystallization solution? This is a quite normal feature, you will find many examples in the PDB.
You could try to model it and see how it fits the density, how your R-factors behave, etc. On Thu, May 16, 2013 at 8:45 AM, Uma Ratu <[email protected]> wrote: > Dear All: > > I collected a data set (1.6A) of one of my target proteins, and built a > model by molecular replacement. > > I then exam the model by Coot and found two unidentified blobs. The two > look the same and not in active sites. > One is close to residues 269 TYR/B and 268 ASN/B, the other is close to 25 > Gly/B and 67 Pro/B. > > The model contains a homo-dimer. The unidentified blobs are only observed > in one monomer, not in the other one. > > I also looked other structures available in this protein family from PDB. > None has this identified blobs in the position as I observed from my model. > > Here is my questions: > 1. How to identify which compound of this electron density is? > 2. Because the blobs are not in the active sites, one should just ignore? > 3. Is it common for unidentified blobs shown in the structure models? > > Attached please find the images of the two blobs. Any clue what it is? > > Thank you for your comments and advices > > Uma > > > -- Mario Sanches http://ca.linkedin.com/in/mariosanches
