Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable
but not quite as bad.
Sorry,
Dale Tronrud
On 08/10/11 15:45, Dale Tronrud wrote:
> I've made a quick look at the model and the paper - and it doesn't
> need more than a quick look. The description of the model in
> the paper sounds great. The problems in the model are clear. My
> favorite is the quote "Trp-477 of PTH1R makes several van der Waals
> contacts with Trp-339 and Lys-337 of G-beta-1 ...". They are "contacts"
> all right. The distances between the 477:CH2 and 337:CE is 2.75 A
> and between 477:NE1 and 339:CH2 is 2.26 A. There are many more.
>
> In general the geometry of this entire model is terrible. In
> Table 1 the bond length rmsd is listed at 1.64 A and the bond angles
> are 0.0078 deg! Perhaps one is to presume the numbers should be
> swapped. In any case, the values I calculate for the model are
> 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists
> the (swapped) values from the paper and then reports hundreds of
> outliers.
>
> The tools proposed by the Validation Task Force should cause a
> model like this to pop out clearly. Even the old tools show this
> model is quite unreliable. We just have to use them.
>
> Dale Tronrud
>
> On 08/10/11 14:35, Jacob Keller wrote:
>> On the surface it doesn't seem as bad as others, i.e., it does not
>> seem to be a real fake--perhaps just a strong form of wishful thinking
>> and creative density interpretation. I wonder what would be a good
>> metric in which to establish a cutoff for present/not present in
>> density. CC, maybe?
>>
>> Jacob
>>
>> On Wed, Aug 10, 2011 at 4:01 PM, David Schuller <[log in to unmask]> wrote:
>>> Time to fuel up the gossip engines for the approaching weekend:
>>>
>>>
>>> http://www.sciencedirect.com/science/article/pii/S096921260800186X
>>>
>>> RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to
>>> the G-Protein Dimer Gβ1γ2
>>> Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094
>>> Structure 2QNS withdrawn.
>>>
>>> --
>>> =======================================================================
>>> All Things Serve the Beam
>>> =======================================================================
>>> David J. Schuller
>>> modern man in a post-modern world
>>> MacCHESS, Cornell University
>>> [log in to unmask]
>>>
>>
>>
>>
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