7 out of 1361 Ramachandran outliers (all prolines) doesn't seem high to me.
________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Oganesyan, Vaheh [oganesy...@medimmune.com] Sent: Monday, April 27, 2015 9:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! 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<UrlBlockedError.aspx> 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.
