-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
This particular model was deposited in early December of 2014, so the authors had the validation report in hand before publication and, I presume could (should) have passed it on to the reviewers. The release date of the entry has nothing to do with the availability of the validation report to reviewers. The model's validation report does have low percentiles on the clashscore and RSRZ outliers but is far better than most 3.5A models for Ramachandran outliers. I'm not sure what your objection to this model is. Did you look at the fit to density and have some specific criticism of the quality of workmanship? As for the PDB releasing a model containing outliers: The PDB is an archive, not a gatekeeper. If you, and your publisher, want to put your name on it the PDB will store it so that others can look at the model/data and judge for themselves. Dale Tronrud On 4/27/2015 7:04 AM, Oganesyan, Vaheh wrote: > Hi Robbie and Co, > > > > These things are happening now too. Look at the entry 4x4m. The > paper got published in January, PDB released coordinates in April. > That means reviewers did not have a chance to look even at > validation report. In my opinion, whatever it is worth, every > journal dealing with crystal structures should, at the very least, > request the validation report from PDB including Nature, Science > and PNAS. > > What is also interesting that at the end PDB released the > coordinates with large number of outliers. I don’t think those can > be justified with low resolution of the data. > > > > /Regards,/ > > / / > > /Vaheh Oganesyan/ > > /www.medimmune.com/ > > > > *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On > Behalf Of *Robbie Joosten *Sent:* Friday, April 24, 2015 2:37 AM > *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] 3BDN, 16.5% > Ramachandran Outliers!!!!! > > > > The PDB_REDO entry for 3bdn was pretty old, so I replaced it using > a newer version of PDB_REDO that can use nucleic acid restraints > from LibG: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html. > Obviously, the new structure model is far from brilliant (PDB_REDO > doesn't rebuild at this resolution), but Molprobity seems to like > it quite a bit more. > > I agree with the replies so far in that: - The topic starter was > rather blunt and could have been more subtle. He should probably go > work in the Netherlands ;) - Building structure models at 3.9A is > incredibly difficult. - The tools we have now are much better than > in 2008. > > However, we should not act like 2008 were still in the dark ages > of crystallography. There are a lot of good structures available > from that time (and also from long before) even at that resolution. > That is not surprising seeing that we also already had very good > building and refinement tools available. We also had enough > validation tools available to tell us that this particular > structure model isn't very good. I really believe that a good > crystallographer that was not pressed for time (or at least didn't > rush) could have done better with the data and the tools > available. > > I'm now going to hide behind an asbestos wall to say this: The > manuscript was submitted in July 29th 2007, the PDB entry was > deposited November 15th 2007. That means that the referees probably > did not have a chance to see the finished structure model, at least > not in the first pass. This implies that the authors didn't want to > deposit the model on time. There are a whole lot of excuses for > this, that are fortunately dealt with now > (http://onlinelibrary.wiley.com/doi/10.1107/S0907444913029168/abstract), > > but the referees could have been a bit more critical. They should have > at least seen that the supplemental table 1 did not show any > Ramachandran statistics. We can only speculate what happened. I'm > guessing that the authors didn't finish the structure yet and > rushed the publication through to avoid being scooped or for the > general glory of a Nature paper. To bad that came at the expense of > the crystallography. > > Cheers, Robbie > > ------------------------------------------------------------------------ > > Date: Thu, 23 Apr 2015 18:43:13 +0000 From: > kell...@janelia.hhmi.org <mailto:kell...@janelia.hhmi.org> Subject: > Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! To: > CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > 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 <mailto: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 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 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> > > > > To the extent this electronic communication or any of its > attachments contain information that is not in the public domain, > such information is considered by MedImmune to be confidential and > proprietary. This communication is expected to be read and/or used > only by the individual(s) for whom it is intended. If you have > received this electronic communication in error, please reply to > the sender advising of the error in transmission and delete the > original message and any accompanying documents from your system > immediately, without copying, reviewing or otherwise using them for > any purpose. Thank you for your cooperation. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU+YvEACgkQU5C0gGfAG10YCACggcfKQ3xRvH6WXd2GdZR37gEJ MH4AoJ0pTexvtBkOYAE/KtwOY0LkUtW1 =E0y1 -----END PGP SIGNATURE-----
