Wei, Did you crystallize your protein in plastic trays? If my memory serves me, there is at least one case of monoamine oxidase B (from the Edmondson and Mattevi groups) where MOAB bound the plasticizer from the wells. You might want to explore that direction as well.
Regards, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: rmgarav...@gmail.com **************************************************************** > On Nov 29, 2016, at 3:26 AM, Wei Liu <we...@me.com> wrote: > > Hi all, > > Thanks for all answers and suggestions to my question regarding the density > for an unknown ligand. Many people raised a possibility that the density > corresponding molecule might locate at a two-fold symmetry axis, but I am > quite sure to rule out this possibility. I tried to placed a molecule of > biphenyl sulfide, which can roughly fit into one half of the density in > question, and performed one round of refinement. As shown in the attached > picture, strong residual density still exist in the rest half, where no > symmetry atoms can be seen. So apparently a real molecule rather than an > artifact lied in this structure, but I am still wondering from where such a > molecule comes and strongly binds to our protein, E. coli or impurities in > the crystallization conditions, as Prem suggested, and if there is any > experimental methods to identify this compound. > > Looking forward to more suggestions. > > Best > Wei > > <Snapshot20161128.png>
