ArticleActa crystallographica. Section F, Structural biology and crystallization communications2012
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen.
Article in Acta crystallographica. Section F, Structural biology and crystallization communications, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
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- A public database of macromolecular diffraction experiments.Acta crystallographica. Section D, Structural biology · 2016Article
- The solvent component of macromolecular crystals.Acta crystallographica. Section D, Biological crystallography · 2015Review
- You are lost without a map: Navigating the sea of protein structures.Biochimica et biophysica acta · 2015Review
- ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.Nucleic acids research · 2015Article
- Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity.The Journal of biological chemistry · 2014Article
- First steps towards semantic descriptions of electronic laboratory notebook records.Journal of cheminformatics · 2013Article
- Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.The FEBS journal · 2013Review
- Unexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine-rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- Trial tests Austrian integrity body.Nature · 2012Article
- Another case of fraud in structural biology.Acta crystallographica. Section F, Structural biology and crystallization communications · 2012Article
- Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen.Acta crystallographica. Section F, Structural biology and crystallization communications · 2012Article
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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, Rσ 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.
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