Hi, Such kind of discussion are really great and fruitful. thanks Pankaj
On Mon, Apr 27, 2015 at 12:25 PM, Dale Tronrud <de...@daletronrud.com> wrote: > -----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----- > -- Pankaj Kumar, PhD
