2HR0
The coordinates for 2HR0 do not form a connected network of molecules in the crystal lattice. The diffraction data do not show the features that should arise from the presence of bulk solvent, whereas the molecular arrangement indicates that large regions are not occupied by protein molecules. The values for ksol and Bsol bulk solvent parameters in 2HR0 are far outside the normally accepted ranges for these parameters. It is also noteworthy that nowhere in the Methods section of his Nature paper is there any mention of non-standard bulk solvent corrections to the Fobs values.

The B-factors of the model do not vary significantly throughout the molecule, even though long segments of the chain are almost completely exposed to solvent (Janssen et al., Nature 448:E1-E2, 2007; note Figure 2 of their communication). The Rfree and R distributions are exceptionally low at low resolution, and the difference between Rfree and R is unusually small for a structure refined at 2.3 Å resolution with an amplitude-based target function. (Janssen et al Nature 9 Aug 2007; note Figure 1b of their communication). Dr. Murthy provided two responses to this allegation: (1) the Rfree and R distribution would be expected if X-ray terms in a restrained refinement were weighted more heavily than usual, and (2) overweighting the X-ray terms would reduce the R-value at the cost of some geometric distortion. Overweighting the X-ray terms can reduce the R-value at the cost of geometric distortion, however, the reported errors in the bond lengths, bond angles and torsion angles all suggest that the geometry was sufficiently restrained during refinement. Furthermore, many of the unrealistic contacts in this structure are far worse than simple geometric distortion.

There are 30 chemically impossible, close contacts shorter than 2.2 Å. Despite the large number of physically impossible clashes, the deposited structure factors show remarkably good correspondence in these regions. Inspection of both the Aσ-weighted 2Fo-Fc and the Fo-Fc electron density maps revealed very well-defined electron densities in every region of bad contacts, with no negative peaks present in the Fo-Fc difference electron density map and with B-factors no higher than elsewhere in the structure. This strongly suggests that the deposited structure factors have been calculated from the structure and do not reflect experimental data. Finally, the range of values for σF is orders of magnitude too large, larger even than the range of structure factor amplitudes. Regarding this point, experimental (“real”) σF values are derived from estimates of measurement uncertainties. For this reason, their values are limited and their range is a small fraction of the range of Fo. However, the range of Fo for 2HR0 is 0 < Fo < 14,215, while the range of σ is 0 < σ < 9948. This range for σ is completely unrealistic. No raw crystallographic data, data reduction output, or any other experimental records that would support the correctness of the structure of 2HR0, or demonstrate that this was an experimentally determined structure, were available for examination.

Actually JBC has already shown it is prepared to do more than most journals on this score (by enforcing retraction of the Gopal Kundu paper against the wishes of the authors and the external committee organised by NCCS, Pune). Will the Nature journals do the same? Or will they continue in their state of unconcerned apathy whereby authors can correct any aspect of their paper but still keep it, no matter how fundamental the problems are (see various recent examples of ‘megacorrections’)