Dear Jacob Keller,
As you say, there is a number of methods used to assign, as correctly as
possible, ions and water molecules:
> depending of everything you know about the purification protocol of
the molecule (every ions and compound which could have been seen by the
target protein),
> depending of the composition of the crystallization drop,
> according to the residual map you observe for the "suspicious" blobs
during the refinement,
> according to the coordinating residues, the coordination number of
the suspected ion, its theorical coordination distances and angles,
> according to the structure factor imaginary part value which can be
increased by choosing the right wavelength for the data collection (see
also the ANODE program, Thorn and Sheldrick, 2011).
But, to my knowledge, there is no automatic evaluation of ion binding
sites during the pdb deposition procedure or in the automated structure
solutions currently proposed in the common refinement programs suites.
Important ion binding sites determination methods could be discussed in
the matching publications...
Best regards.
Romain.
Le 06/03/2014 20:56, Nat Echols a écrit :
On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob
<[email protected] <mailto:[email protected]>> wrote:
I was curious whether there has been a rigorous evaluation of ion
binding sites in the structures in the pdb, by PDB-REDO or
otherwise. I imagine that there is a considerably broad spectrum
of habits and rigor in assigning solute blobs to ion X or water,
and in fact it would be difficult in many cases to determine which
ion a given blob really is, but there should be at least some
fraction of ions/waters which can be shown from the x-ray data and
known geometry to be X and not Y. This could be by small anomalous
signals (Cl and H2O for example), geometric considerations, or
something else. Maybe this does not even matter in most cases, but
it might be important in others...
A couple of references:
http://www.ncbi.nlm.nih.gov/pubmed/18614239
http://www.ncbi.nlm.nih.gov/pubmed/24356774
Anecdotally, it is not difficult to find incorrect structures; in
fact, one of mine has "magnesium" ions at crystal contacts with big
Fo-Fc and anomalous map peaks, and I know it's not the only such
structure in the PDB. However, while there are plenty of examples that
are clearly wrong, it is difficult to come up with strict rules that
apply to typical MX data - at 3Å resolution (or even better), a native
Zn-binding site might have bond valences that are just awful. This
doesn't mean the metal assignment is wrong. The placement of waters
alone has a huge impact on such calculations.
-Nat
