Is it in pdb redo? Take a look here: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html
JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Misbah ud Din Ahmad Sent: Thursday, April 23, 2015 2:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! 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<mailto: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<tel:%28%2B34%29%2091%20585%204616> 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<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf of Mark J >> van Raaij [mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>] >> Sent: Thursday, April 23, 2015 11:49 AM >> To: CCP4BB@JISCMAIL.AC.UK<mailto: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 >>> >>> >>> >>> >>> >>> >>> >
