Elaborating on Phoebe's answer, the question to ask is : "is the structure good enough to support the conclusions reached in the paper" ? That is, quoting the abstract : "an unusual overall architecture that allows it to adopt a conformation that appears to facilitate pairwise cooperative binding to adjacent operator sites".
The answer is yes. Another question could be: "does the structure provides an accurate picture of the structure, within a 0.2Å positional error". The answer is no. But then the authors made no such claim. Thierry From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A. Rice Sent: Thursday, April 23, 2015 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! Dear Misbha, Before you throw stones at other peoples' work: - have YOU tried to refine a structure at 3.9A, particularly with older software? - there are many structures in the database that are related to lambda repressor. Have you checked how the structure in question compares to those determined at higher resolution? Is the overall fold the same? Is the sequence register the same? Remember that it is unreasonable to expect that all the side chain rotamers will be correct at 3.9A. - When you looked at the actual electron density, what, exactly, did you see that suggested the structure may not be correct? - The structure factors were deposited, so it should be easy for you to try re-refining it yourself with newer software, and see if it makes much difference to the final model. - If you've gone through all those steps, and are still convinced that this structure is problematic, please do let the community know! ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Misbah ud Din Ahmad [misba.ah...@gmail.com] Sent: Thursday, April 23, 2015 11:03 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! 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 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
