Dear Mengxiao, From my experience I would say that the two e. densities (blob1 and blob2) are present the same molecule.
What that might be is more difficult to answer. Based in the concentration you gave us and the electron density volume I would say that is more likely to be ammonium sulphate (NH4 and SO4). As you say the lower part looks like SO4 and make sense to interact with Arg, Lys and Asn and the other end looks like NH4. But those two group there and give it one round of refinement. Check the B factors at the end Do they make sense (directions of H-bonds, distance between NH4 and SO4)? Is the Bfactor similar for NH4 and SO4 They should not have a difference greater than 50%. You could try also Na in stead of NH4 George _____ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of mengxiao lv Sent: Tuesday, February 10, 2009 7:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unknown density for a small molecule 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
