Dear Phoebe A. Rice, I didn't mean to discredit the work but the statistics of the structure just shocked me at the first instance. I could for example point out to another structure 1ZR2, which has the same resolution (the protein Molecular weight is almost the same) and the statistics are: R-work: 0.27 Rfree: 0.319 Ramachandran outliers: 2.8%
The structure was solved by a combination of MIR and MAD three years earlier in 2005 and definitely they didn't had better softwares. As per your advice, I tried one cycle of refinement of this structure in Phenix and the statistics are: Start R-work = 0.2816 ; Start R-free =* 0.3551* Final R-work = 0.2887 ; Final R-free = *0.3671* Ramachandran outliers: 18.91% Rotamer Outliers: 25.19% Being a crystallographic community, isn't it our responsibility that if better softwares are available now, we try to re-refine our older structures and deposit better models in the PDB. That would help the users immensely. Misbha On Thu, Apr 23, 2015 at 7:06 PM, Mark J van Raaij <mjvanra...@cnb.csic.es> wrote: > 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 > >>> > >>> > >>> > >>> > >>> > >>> > >>> > > >
