Covering your Tracks
is a good idea if you think people are on to you. Eric points us to the communication in Nature that brought into question PDB entry 2HR0 (background posts: here and here). The reply was also published in Nature with the authors standing by their data. The 30-40 Angstrom gaps are explained by citing a personal communication with W. A. Hendrickson as well as the presence of protein fragments that serve as disordered lattice contacts.
The possible location of the protein fragment is shown in the reply.
Below is a display of the protein packing without the ‘protein fragments’ that served as the lattice contacts.
The figure below, shows additional symmetry related proteins, gaps occur vertically (in the c-direction) and are noted with a red circle.
Artem notes that they could have done a better job fabricating the data. We all Most of us try to learn from our mistakes and correct them, if possible.
Learning from your mistakes:
A glaring problem with the 2HR0 structure was the existence of these gaps. You can come to your conclusions on whether you believe there are disordered lattice contacts. However, what would greatly undermine their credibility would be if they had deposited another structure that contained these unusual gaps.
This brings us to the structure 2OU1, but wait. This structure doesn’t have very large gaps…
They learned.
If you take a close look at the PDB entry you will notice that this structure was updated (see Deposition Summary: right side, under the picture of the molecule). The structure that was initially deposited with the PDB entry 1L6K.
Here is the textual comparison:
The major change is shown with the red arrow above noting that the c-axis was nearly cut in half.
Why update?
Covering their Tracks:
The crystal packing of 1L6K:
The gaps… ~30 Angstroms, sound familiar?
The crystal packing of 2OU1:
The gaps have been significantly reduced.
They learned from their mistake in the 2HR0 entry. The large reduction in the length of the c-axis results in more reasonable crystal packing.
Time line:
The PDB entry 2HR0 was initially released at the end of October in 2006. The initial correspondence questioning the structure and reply were published in August 2007.
The original structure PDB entry 1L6K was deposited in 2002. The update of this structure was in February of 2007. It would be interesting to know when the authors were contacted about 2HR0.
One explanation is that once they were contacted about the 2HR0 structure, they realized there was a similar issue with 1L6K and replaced it with 2OU1.
As with the hypothesis about the entry 1BEF, I do not have any proof that this is what is going on, but definitely thought it was worth mentioning.
What do you think? Sound reasonable?