Hi Dale, The data looks fine but the refinement for 3kj5, 2qns's 'improved' model, is still pretty poor. Looking at the EDS maps for this entry there is some (model bias) density for the ligand but, it is clearly not there. The PDB_REDO optimization (http://www.cmbi.ru.nl/pdb_redo/kj/3kj5/index.html) improves the model substantially (with the exception of the Ramachandran plot) and removes pretty much all the density of the ligand. I'd say it's clear that 3kj5 was poorly refined, and that proper refinement would have made it very clear that the ligand isn't there. I just hope that nobody cited the structural aspect of the paper.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Dale Tronrud > Sent: Thursday, August 11, 2011 18:13 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Another paper & structure retracted > > It is my understanding that there is no "retracted" category in the wwPDB. > Models are "obsoleted", usually with a replacement but sometimes without. > I don't know of a way to distinguish between those models obsoleted for > gross error and those simply replaced by one of higher quality. Surely this > is a > continuum. > > In the current case, I've seen nothing to suggest that the diffraction > data is > bad, although I've not looked at it hard, so the model's creator could run a > proper refinement and submit a replacement. This model is so poor that I > can't be sure, but I suspect that that model would be an apo form and > probably of little interest. This is a good case for an "obsolete without > replacement". > > I should note that, while the paper has been retracted, I see no indication > that the entry 2QNS has been "obsoleted". Perhaps that update is still in the > pipeline. > > Dale Tronrud > > On 08/11/11 06:46, Garib N Murshudov wrote: > > Dear all > > > > Does anybody have the list (pdb as well as structure factors) of all > > retracted structures? > > > > regards > > Garib > > > > On 10 Aug 2011, at 22:01, David Schuller wrote: > > > >> Time to fuel up the gossip engines for the approaching weekend: > >> > >> > >> http://www.sciencedirect.com/science/article/pii/S096921260800186X > >> > >> RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus > >> Bound to the G-Protein Dimer Gβ_1 γ_2 Structure, Volume 16, Issue 7 > >> > <http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23 > T > >> > OC%236269%232008%23999839992%23693753%23FLA%23&_cdi=6269&_pub > Type=J&v > >> > iew=c&_auth=y&_acct=C000022719&_version=1&_urlVersion=0&_userid=49 > 213 > >> 7&md5=9dc4b8953d3fa243dc98e395b6ac590d>, > >> 9 July 2008, Pages 1086-1094 > >> Structure 2QNS withdrawn. > >> -- > >> > ========================================================== > =========== > >> == > >> All Things Serve the Beam > >> > ========================================================== > ============= > >> David J. Schuller > >> modern man in a post-modern world > >> MacCHESS, Cornell University > >> schul...@cornell.edu > > > > Garib N Murshudov > > Structural Studies Division > > MRC Laboratory of Molecular Biology > > Hills Road > > Cambridge > > CB2 0QH UK > > Email: ga...@mrc-lmb.cam.ac.uk > > Web http://www.mrc-lmb.cam.ac.uk > > > > > >
