Nice paper ! I really wish PDB could have some people to review those important structures, like paper reviewer. If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated.
The worst case is: 1. All of data was correct and real, 2. The key structural evidence (< 1%) was not presented or excluded in the discussion. 3. Then the paper was reviewed by some famous people, and then published on those top level journals. 4. Eventually, it is cited in our textbook for years. For the most of cases, reviewer and reader will mainly rely on graphics displaying only. It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. Recently, I have seen several stories like this. Here is an open letter to Nature. http://www.jinkai.org/AAD/AAD_letter_2_nature.html I hope you experts will also check the coordinate files for verification. Sincerely, Kevin On Sat, Mar 31, 2012 at 8:26 AM, Bosch, Juergen <jubo...@jhsph.edu> wrote: > really fascinating, bringing back the discussion for a repository for your > collected frames. > > Jürgen > > > *Acta Cryst.* (2012). F*68*, 366-376 > doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421> > * > * > Detection and analysis of unusual features in the structural model and > structure-factor data of a birch pollen allergenB. > Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.> > > *Abstract:* Physically improbable features in the model of the birch > pollen structure Bet v 1d (PDB entry > 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) > are faithfully reproduced in electron density generated with the deposited > structure factors, but these structure factors themselves exhibit > properties that are characteristic of data calculated from a simple model > and are inconsistent with the data and error model obtained through > experimental measurements. The refinement of the > 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model > against these structure factors leads to an isomorphous structure different > from the deposited model with an implausibly small *R* value (0.019). The > abnormal refinement is compared with normal refinement of an isomorphous > variant structure of Bet v 1l (PDB entry > 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). > A variety of analytical tools, including the application of Diederichs > plots, *R*[image: [sigma]] plots and bulk-solvent analysis are discussed > as promising aids in validation. The examination of the Bet v 1d structure > also cautions against the practice of indicating poorly defined protein > chain residues through zero occupancies. The recommendation to preserve > diffraction images is amplified. > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > > > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/
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