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 >> >> >> >> >> >> >>
