Another thing to consider is alternate ligand conformation. The water density (elongated) and the pocket composition (aromatic) could result in two alternative binding orientations (of the buffer? I need 3D). I would play around with models to see if it fits the density.
Paula Lario #778-828-3701 On Jul 9, 2010, at 5:12 AM, Nick Quade <nick.qu...@helmholtz-hzi.de> wrote: > Dear CCP4 community, > > I have solved the structure of a protein in complex with DNA. But, inside the > protein there seems to be a ligand binding pocket with some strong density > (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The protein > was in Tris buffer, with some NaCl, MgCl2 and DTT and crystallized in Li2SO4 > with MES. What could this density be? I can exclude MES as crystals grown > with citrate buffer have the same density. So I guess it might be something I > co-purified or perhaps some degradation product of the DNA? The electron > density in the pictures is at 1.5sigma. > > Thanks in advance. > > Nick
