The methods part of the 2008 nature paper also mentioned the two earlier,
high-res structures 1F39 (1.9 A) and 1LMB (1.8 A), which together cover
almost the whole strucutre except the linker regions.
I wonder, in such situations, is it a good practise to use the high res
structures, either as referenece structures or as start points for
refinement, to improve the low res structures? I have no doubt that most
people would give both a try and compare the results. But what are people's
opinions on publishing the resulting low res structures that contain
significant amount of information coming from prior high-res strucutures? In
which way should we think: "this gives better structure so that the user
sees less artifact" or, "no, this introduces information that did not come
from my data"?
Zhijie
-----Original Message-----
From: Mark J van Raaij
Sent: Thursday, April 23, 2015 1:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
The abstract of the papers says they used MIR.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 23 Apr 2015, at 18:57, Todd Jason Green wrote:
My guess is they had the best data they could get, did molecular
replacement with the two halves of the repressor and the dna, got a
solution and didn't use appropriate restraints in the refinement. Like
Phoebe mentioned, we have better tools for this these days.
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J van
Raaij [mjvanra...@cnb.csic.es]
Sent: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
How reliable is too general a question - it depends on what you want to
know.
At 3.9Å they could probably place the phosphate atoms quite well and see
the general fold of the protein.
Finer details will be less reliable, i.e. where the exact side-chains are
etc.
They could probably have forced more amino acids into favourable
Ramachandran angles, but would that have made the structure "better"?
Would these favourable angles have been more "right"? At 3.9Å you can't
know for sure.
Would they have been able to draw more biological conclusions? I'd say
not.
As long as they do not draw more conclusions in the paper than what is
supported by the medium-resolution data, the structure provides useful
information.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 23 Apr 2015, at 18:03, Misbah ud Din Ahmad wrote:
Dear crystallographers,
The PDB entry
http://www.rcsb.org/pdb/explore.do?structureId=3BDN
has 16.5% Ramachandran outliers. When I opened this PDB file in coot and
checked for Ramachandran outliers, the results are:
In preffered region: 58.04%
In allowed regions: 19.78%
Outliers: 22.17% !!!!!!!!!
With an R-free of 37.4% at 3.9 A resolution, could you please tell me how
reliable this structure of Lambda repressor bound to DNA is?
Thanks
Misbha
