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 <dj...@cornell.edu> 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 Structure 2QNS withdrawn.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 >>> schul...@cornell.edu >>> >> >> >>
