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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 > > > > > > >