I really don't think that 22% R-free AT 2.0 Å constitutes "gross
disagreement" barring deliberate data manipulation, although it doesn't
eliminate the possibility of significant errors in lower quantities.
The review-quality validation report should report bad fits to density
(although somewhat exaggerated at time) but I don't think it has an
assay of difference density peaks (say >5 sigma) that were not fit.
Perhaps a coot-like list of unmodelled blobs would be a worthy addition.
I doubt the validation protocol would find, e.g., mis-assignment unless
it happened at a large scale, and the areas that it's more likely to
occur (partly disordered) aren't going to show a strong signal. Hard to
replace the human brain when trying to interpret ambiguous regions.
Phil
Princeton
On 6/2/25 9:05 AM, Oganesyan, Vaheh wrote:
Hello,
All suggestions on what and how to handle this case are good. However,
aren’t we missing a major point?
How could a model that exhibits gross disagreement with data be allowed
in PDB? Isn’t validation protocol created to prevent cases like this?
Vaheh
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Nikolas
*Sent:* Friday, May 30, 2025 5:31 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] How to address deposited structures poorly modeled?
*enters the BB and kneels in reverence*
Dear BB,
Recently, delving among papers and structures for a current project, I
came across a deposited structure of interest that is terribly modeled.
In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the quality
indicators are not terrible but upon opening it and checking the maps
there are some severe mistakes in the modeling.
For instance, a full chain that is in the negative Fo-Fc while positive
density is present, some density that is quite clear for SO4 molecules
(buffer) modeled as water and density for water molecules neglected.
Some parts seem like “coot:runwater” has been used and not checked. The
catalytic site is well defined.
Now, I’ve started my journey in crystallography not too long ago and
I’ve got many years, structures to solve and things to learn, and I know
that sometimes the dataset “is what it is” but these seems quite big
mistakes. Especially because I’ve worked with such proteins before and I
know the systems.
My question thus is: would it be right to contact the author of this
structure and point to these issues? What’s the best way to address such
things, possibly without coming off as obnoxious?
Thank you for your wisdom.
Cheers,
Nikolas
*bows and leaves the BB*
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