Hi, It could be all sorts of things, but the one that for some reason is stuck in my mind is isopentenyl phosphate (phosphate, not pyrophosphate!). Of course w/o seeing the density in 3D this is just a guess.
Artem > Dear All, > > When I was refining my structure, I found some unmodeled blobs, shown as > attached images (contoured at 3 sigma for Fo-Fc, Rfree 0.21 and Rfactor > 0.18, refined to 1.9 angstrom ). > > The protein was expressed in E.coli and purified by nickel column and gel > filtration, both in tris buffer. The crystallization condition has 2 M > ammonium sulfate and 0.1 M sodium acetate. > > The lower part looks like a sulfate group, which is held by one Arg, one > his, one lys and one asn. The latter three residues are from another > asymmetric unit. > > The other end of the small molecule is stunk by the rings of Tyr and Phe. > It > also interacts with the OH group of another tyr and one water molecule. > > Is there a program can build small molecule models according to the > densities? Or could anyone tell what it might be from the density? > > Thanks a lot! Any suggestions will be appreciated! > > Mengxiao >
