To butcher an immortal phrase: all models are wrong, but some models are 
more wrong than others. A while back I came across this quite amazing 
feature in a 1.28 Angstrom structure!

This does bring up a question: is the wwPDB formulating a policy on what 
to do regarding correction of structures where the original authors are 
no longer with us?


On 2017-06-27 08:35, Goldman, Adrian wrote:
> There are plenty of such structures in the PDB. We have one that we
> are rerefining at the moment - and indeed there is a whole slew of
> structures from the same author, all done sloppily. Here’s an
> example of a 2 Å (!) structure. The Tyr clearly goes into the green
> blob above it, and the loop conformation is all wrong.
> 
> I think the issue may be that there are too many people out there
> “solving structures” who actually have very little skill at doing
> so.
> 
> Adrian
> 
> loopth
> 
>> On 27 Jun 2017, at 10:15, Trevor Sewell <[log in to unmask]>
>> wrote:
>> 
>> The misinterpretation is considerable I as can be seen from the
>> attached coot screenshot.
>> 
>> I have no reason to suspect malfeasance. But it looks like the
>> authors didn’t check very carefully.
>> I have re-interpreted and refined the density and it is just fine
>> – Rfactor of 18% for a 2.3A structure.
>> 
>> The critical reinterpretations concern the orientation of the
>> backbone near the active site and the interpretation of a blob of
>> density claimed to be substrate in the original paper.
>> 
>> Maybe the best would be to write to the author and suggest that she
>> obsolete the structure. We could see if we could reach some
>> agreement on how to take it further – perhaps a letter to the
>> editor of JBC.
>> 
>> Sent from Mail [2] for Windows 10
>> 
>> FROM: Manfred S. Weiss
>> SENT: Tuesday, June 27, 2017 8:46 AM
>> TO: Trevor Sewell
>> SUBJECT: Re: [ccp4bb] Incorrect Structure in the PDB
>> 
>> Dear Trevor,
>> 
>> you can download the incorrect structure and the associated data
>> and reinterpret and
>> re-refine the structure. Then you can re-deposit provided you write
>> a paper about the
>> new findings. This is currently the policy of the PDB.
>> 
>> Else, you can contact the authors of the incorrect structure and do
>> the reinterpretation
>> together with them? They can replace the incorrect structure
>> without a new publication.
>> 
>> That's all there is at the moment.
>> 
>> May I ask what is incorrect about the structure?
>> 
>> Cheers,
>> 
>> Manfred
>> 
>> Am 27.06.2017 um 08:34 schrieb Trevor Sewell:
>> 
>>> I have come across a key paper in my field that describes an
>>> enzyme mechanism. Their work is based on a deposited structure –
>>> by other authors - that is incorrectly interpreted.
>>> 
>>> Is there a process for removing a demonstrably wrong structure
>>> (deposited by others) from the PDB and replacing it with a
>>> correctly interpreted structure based on the original data? Or is
>>> there an alternative, and generally recognized, way of getting the
>>> correct structure in the public domain?
>>> 
>>> Many thanks for your advice on this matter.
>>> 
>>> Trevor Sewell
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>> 
>> --
>> Dr. Manfred S. Weiss
>> Macromolecular Crystallography
>> Helmholtz-Zentrum Berlin
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>> D-12489 Berlin
>> Germany
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>> [log in to unmask] <Around residue 228.png>
> 
> 
> 
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