Dale, This is exactly the conversation I just had with my student Jason, right on! The paper we are writing just now, this is figure 1. But I always get rejected by Nature, so go figure. On Thu, Aug 11, 2011 at 1:25 PM, Dale Tronrud <det...@uoxray.uoregon.edu>wrote:
> I agree with Prof. Tomchick: if the point of your paper is your crystal > structure of > the binding of a ligand to a protein you should include a figure with the > omit map > (displayed without a "cover radius") that convinced you that binding took > place. I > prefer that map over some simulated, after-the-fact, omit map calculated > just for > publication. > > This is not simply a matter for reviewers to be gatekeepers, it is > important for the > readers to know what level of confidence to place in this result, and it is > instructional > for everyone to see what ligand binding density looks like. Apparently > some people don't > know what features to look for to distinguish between signal and noise. > > Dale Tronrud > > On 08/11/11 09:40, Diana Tomchick wrote: > > A quick glance at the header of the PDB file shows that there is one > glaring discrepancy between it and the table in the paper that hasn't been > mentioned yet in this forum. The data completeness (for data collection) > reported in the paper is 95.7%, but in the header of the PDB file (actually, > in both the 2QNS and the 3KJ5 depositions) the data completeness (for data > collection) is reported as only 59.4%. The PDB header also contains an > inconsistency, with the data completeness (for refinement) reported as > 95.7%. Since the numbers of reflections reported for refinement versus data > collection in the PDB header differ by less than 1%, it appears that there's > been a bit of magical thinking that took place somewhere along the process > from data processing to final model refinement. Small wonder that the > refined geometry is so poor. Perhaps if these scientists had actually > collected a complete dataset, we would not be having this conversation. > > > > Diana > > > > P.S. I have, on occasion, provided the coordinates and a map file to > reviewers when they requested it. The last time it was requested was many > years ago; I decided it was safer and easier if I provided as much > information as possible in the manuscript (including better quality electron > density figures than appear in this paper) to allow the reader to determine > whether the work is valid or not. > > > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > Diana R. Tomchick > > Associate Professor > > University of Texas Southwestern Medical Center > > Department of Biochemistry > > 5323 Harry Hines Blvd. > > Rm. ND10.214B > > Dallas, TX 75390-8816, U.S.A. > > Email: diana.tomch...@utsouthwestern.edu > > 214-645-6383 (phone) > > 214-645-6353 (fax) > > > > > > > > On Aug 10, 2011, at 5:45 PM, 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 > >>>> > >>> > >>> > >>> > > > > > > ________________________________ > > > > UT Southwestern Medical Center > > The future of medicine, today. >
