[phenixbb] green ball in aspartate

Nathaniel Echols nechols at lbl.gov
Thu Oct 30 23:10:47 PDT 2014

On Thu, Oct 30, 2014 at 6:51 PM, Murpholino Peligro <murpholinox at gmail.com>

> 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.

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