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: [log in to unmask]
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 [[log in to unmask]] on behalf of Mark J van
> Raaij [[log in to unmask]]
> Sent: Thursday, April 23, 2015 11:49 AM
> To: [log in to unmask]
> 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
>>
>>
>>
>>
>>
>>
>>
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