Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

[Gert Vriend]

At around 4.0 A resolution one normally cannot talk about accuracy. The 
density will at most locations not warrant any detailed interpretation. 
If, at 4.0 A resolution, you move atoms around a bit, you will not see 
significant changes in R/Rfree. So, you can do whatever you want, more 
or less. If the refinement puts great emphasis on the secondary 
structure (i.e. tries to force the Ramachandran plot, then you get a 
good Ramachandran plot, but if they put more weight of the fit to the 
density, you get a slightly lower R (and perhaps even Rfree) at the cost 
of the Ramachandran plot. And all of that is meaningless.
At this resolution you have to check if the fold is likely to be 
correct. I superposed just any high(er) resolution domain with high 
sequence similarity at the corresponding 3bdn domain, and I take any bet 
that the fold of 3bdn is right (at least of the domain I looked at, and 
I extrapolate to the other domain).
PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/) cannot improve this one, and 
WHAT_CHECK (http://swift.cmbi.ru.nl/gv/pdbreport/) throws its hands up 
in the air. At 4.0 A you should be happy with an indication of the fold 
(and with the fact that the authors probably went through great pains 
for you getting these coordinates close to where they should be).

Gert