I agree you should describe, and deposit what you have along with the
experimental data.
Then if anyone really wants to examine the structure in more detail,
they can.
Perhaps we need an extra PDB record (ILLDEF - for ill-defined )
Eleanor
Richard Gillilan wrote:
I'm sure many of you have been in this situation before, so I would be
interested in your opinion.
I'm about to submit a paper containing the structure of a liganded
protein. The ligand itself is rather uninteresting, but it induces an
important conformational change. I solved a second structure
containing another different ligand which induces the same
conformational change. Sadly, stereochemical inhomogeneity in the
ligand results in poorly defined and ambiguous ligand density,
nonetheless, the conformational change is very distinct and
well-defined in the omit map (even better than the first ligand). My
inclination is to at least mention the results, if not include them
in, say, the supplementary materials to the paper. The structure is
not technically necessary to the case, but would strengthen the
argument. I don't feel that the ligand density is well resolved enough
to warrant deposition.
How much would you, as a reader, want to see? Crystallization
conditions, unit cell, space group? Omit maps with very
partially-built ligand? Nothing at all?
Richard Gillilan
MacCHESS
Cornell
