I would have thought that ligands are ligand/ion?. What I have just
done with a recent structure and I await the reviewers noticing or not
is include the ethylene glycol from the cryo that I can (probably) see
in a solvent (rather than water) atom number and bfactor line along with
water (which probably includes sodium/chloride ions etc misassigned as
water) rather than as ligand.
I would suggest that Protein, Ligand, Solvent/Ion is probably a better
break down than Protein, Ligand/Ion and Water alhtough if I had an ion
associated with a ligand Mg on my ATP I would have that in ligand
rather than ion. What then should you do if there are waters then
visible on the ion???
I guess the question that this is really asking is whether the Bfactor
of what you are describing as a significant ligand in your discussion is
well ordered compared to the surrounding protein.
Gubbins filling out density peaks in the "solvent area probably should
not be included in that line.
Best wishes
Nick
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck, University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX
email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852 (Room G54a Office)
020-7631-6800 (Department Office)
Fax 020-7631-6803
If you want to access me in person you have to come to the crystallography
entrance
and ring me or the department office from the internal phone by the door
