Hi Francis,
Even though they are not published, there are enough models in the PDB for
which reevaluation of the crystallographic data leads to new biological
insight. Unfortunately, a lot of the insight is of the type "that ligand
doesn't really bind, or at least not in that pose". Another nice one is a
sequencing error in a Uniprot entry that became obvious after critically
looking at the structure and the maps (the authors, of both structure and
sequence, acknowledge the problem, but the entry is not yet fixed, so no
names). Yesterday, I had a case where I didn't so much mistrust the model,
but I would still have liked to have access to the images. There was
something weird in the maps that was also clearly there in pictures of the
maps in the linked publication, but it was not discussed.
Needless to say, I'm in favour of depositing images. At least for published
structure models. There is still a lot of interesting things to find in
current and future PDB entries.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> James Stroud
> Sent: Friday, October 28, 2011 07:57
> To: [log in to unmask]
> Subject: Re: [ccp4bb] raw data deposition
>
> On Oct 27, 2011, at 5:22 PM, Francis E Reyes wrote:
> > So I ask again, are there literature examples where reevaluation of the
> crystallographic data has directly resulted in new biological insights
into the
> system being modeled?
>
> This is a poor criterion on which to base any conclusions or decisions. We
can
> blame the lack of examples on unavailability of the data.
>
> Right now, I'd love to get my hands on the raw images for a particular
cryoEM
> data set, but they are not available--only the maps. But the maps assume
> one symmetry and I have a hypothesis that the true symmetry is different.
I
> could test my hypothesis by reprocessing the data were it available.
>
> James
|