On Thu, Oct 30, 2014 at 6:51 PM, Murpholino Peligro <murpholinox@gmail.com> wrote:
Does anybody knows what could this be?
Blue map at 1rmsd
Green and red map at 3.5 rmsd
Purple map (FEM map) at 1rmsd

Conditions 100mM sodium acetate, NaCl 10% w/v, cryo=glycerol 30 % v/v; protein is hen egg white lysozyme (usual condition, usual protein and ohh..almost forget it.. ascorbic acid at 0.5 M)

A water molecule overlaps with the oxygen atom (OD1) of the aspartate residue. So it is not a water molecule.
Any ideas? (In coot -> validate-> difference map peaks and holes-> its the only one at 7.7 rmsd)

Jane Richardson's advice for cases like this is that it's probably sodium - obviously it's missing the rest of the coordination shell, but there still isn't anything else that I can think of that makes sense chemically.  Try placing a sodium there and running another round of refinement, and see what happens to the B-factors.  If the "sodium" ends up with significantly lower B-factors than the Asp sidechain or the rest of the protein, that would tend to indicate something heavier.  If you get negative difference density, try refining occupancy as well.  If you still have positive density, it's almost certainly something else.

In your particular case I would also try downloading all HEWL structures in the PDB at similar-or-higher resolution and the same crystal form, and looking at that site - it is possible that someone else has seen the same feature before.

-Nat