On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote:
> Dear all,
>
> I was looking at a 3 angstrom structure from 2015 with relatively bad
> statistics, so I decided to look at the pdb-redo of said structure.
> Surprisingly, pdb-redo statistics are even worse.
You say "even worse", but the subset of statistics you show does not
look so bad for a 3A structure either before or after re-refinement.
Other than maybe the Rfree itself, which is what you ask about.
> As you can see on the
> attached picture, the pdb-redo Rfree comes with a caveat:
>
> R-free was considered biased, the estimated unbiased R-free was used
>
> I understand that the R-free was considered biased because a new (Rfree)
> test set was determined. However, I'm not sure what is the unbiased R-free
> is / how it is calculated in this case?
>From the "How does it work" page on the PDB Redo web site,
my understanding is that rather than calculating Rfree from the
re-refinement, various other quality measures are used to
calculate an expected Rfree/R ratio consistent with other
structures of similar quality.
This ratio is then multipled by R to yield an estimated Rfree.
Robbie Joosten will probably correct me if I have that wrong :-)
cheers,
Ethan
>
> Thanks in advance,
>
> Best,
>
> Nadia
--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
