Sorry, I don't quite understand your reasoning for how the structure
is rendered useless if one refined it with all data.
Would your argument also apply to all the structures that were refined
before R-free existed?
Quyen
You should enter the statistics for the model and data that you
actually deposit, not statistics for some other model that you might
have had at one point but which the PDB will never see. Not only
does refining against R-free make it impossible to verify and
validate your structure, it also means that any time you or anyone
else wants to solve an isomorphous structure by MR using your
structure as a search model, or continue the refinement with higher-
resolution data, you will be starting with a model that has been
refined against all reflections. So any future refinements done
with that model against isomorphous data are pre-biased, making your
model potentially useless.
I'm amazed that anyone is still depositing structures refined
against all data, but the PDB does still get a few. The benefit of
including those extra 5% of data is always minimal in every paper
I've seen that reports such a procedure, and far outweighed by
having a reliable and relatively unbiased validation statistic that
is preserved in the final deposition. (The situation may be
different for very low resolution data, but those structures are a
tiny fraction of the PDB.)
-Nat
