Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen by B. Rupp
Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 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 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). A variety of analytical tools, including the application of Diederichs plots, R 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.
And the response from the authors:
Acta Cryst. (2012). F68, 377 [ doi:10.1107/S1744309112008433 ] Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen by N. Zaborsky, M. Brunner, M. Wallner, M. Himly, T. Karl, R. Schwarzenbacher, F. Ferreira and G. Achatz
Synopsis: A response to the article by Rupp (2012), Acta Cryst. F68, 366-376.
This case further documents aspects related to the need for diffraction data images availability.
The call for a 'universal system' by the Acta Cryst D and F Editors:
Acta Cryst. (2012). F68, 365 [ doi:10.1107/S1744309112011852 ] Another case of fraud in structural biology by M. S. Weiss, H. Einspahr, E. N. Baker and Z. Dauter
relates to much of what this IUCr Forum has also been discussing. The possibility of local raw data repositories (with each data set DOI registered where it underpins a publication) being explored by the IUCr DDD WG is unlikely to be ‘universal’ in its global coverage.
Nevertheless, although this may not provide a 'universal solution', any responsible research-led university should be interested in making sure that a raw data archive is available for its research staff, and should have experience in DOI registration of raw data sets (or be able to advise its research staff how to get DOIs). This challenge would be eased by SR and neutron facilities archiving raw data measured at those facilities, as is beginning to be the case, at least, as far as we know in Europe and Australia.
Setting standards by encouraging such archives will afford a much needed clarity in favour of retaining raw data wherever possible. A separate issue will be the certain expansion of current validation checks. Already it is the standard practice in chemical crystallography submissions to IUCr journals for Co-Editors to validate the structure determination and refinement.
We again encourage colleagues to lodge their inputs on this IUCr Forum on any aspect of principle or practice in achieving diffraction raw data archiving.
John R. Helliwell, Tom Terwilliger and Brian McMahon