Blobology (a branch of macromolecular crystallography).
You could maybe place benzoate in there (the 6 membered ring on "top" in
the pictures), refine, compute a new map and see if you can make
something out of it. Why benzoate: because the ring would find its place
nicely in the "hydrophobic" environment, especially the TYR and TRP side
chains. If it does not make sense (difficult to say from pictures, I
tried rotating by to no avail...) then place a few waters, refine and
see if the new density makes sense after refinement.
Fred.
Nick Quade 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
