Thanks for your quick responses. I used ethylene glycol as cryoprotectant. Indeed I had 1% DMSO as part of the crystallisation condition (I forgot to include that), but DMSO is too small to fit this density and DMSO has a trigonal pyramidal structure, which differs a bit to what I have in my structure.
On Mon, May 14, 2018 at 11:12 AM, Ethan Merritt <[email protected]> wrote: > On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote: > > Dear all, > > > > I am currently refining a structure and found a intriguing electron > density > > at the protein surface (pictures attached, the Fo-Fc map is contoured at > > >3.5 sigma). My first candidates were molecules from my protein prep or > > crystallisation buffer, but none of them seem to fit well. I can observe > > that the ligand is nearby the side chains of a tyrosine, a lysine, a > > threonine and a glutamate residue, and it is close to the carbonyl > oxygens > > of the protein backbone of a nearby loop. The shape of this density is > not > > pyramidal, but it is not planar either. > > > > Do you have any suggestions to solve this density based on your own > > experience? My crystallisation buffer contains tartrate, ammonium > sulphate, > > and CHES, and my protein is in Tris buffer containing DTT and sodium > > chloride. > > DMSO? > > > > > > Best regards, > > > > > > -- > Ethan A Merritt, Dept of Biochemistry > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > -- Mario Daniel García
