Open AccessDetection and analysis of unusual features in the structural model and structure‐factor data of a birch pollen allergen
Author(s) -
Rupp Bernhard
Publication year - 2012
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
ISSN - 1744-3091
DOI - 10.1107/s1744309112008421
Subject(s) - protein data bank (rcsb pdb) , r value (soils) , pollen , protein data bank , crystallography , diffraction , protein structure , biological system , chemistry , physics , biology , geology , botany , soil science , optics , stereochemistry , biochemistry , soil water
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 σ 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.