Comments on: Covering your Tracks

By: Eric Williams

Eric Williams — Wed, 06 Jan 2010 21:00:22 +0000

Boy, it sure would be nice if the PDB reported why an author chose to obsolete a model.

By: Aaron

Aaron — Thu, 17 Dec 2009 23:33:41 +0000

Sean, I think he was referring to a previous poster…

By: Sean

Sean — Thu, 17 Dec 2009 05:02:37 +0000

Hi Nico,

No need to be a Devils advocate

My goal with this post was to show the connection between the unusual packing feature between these two structures and not to repeat the Nature communication.

By: Nico

Nico — Thu, 17 Dec 2009 03:57:10 +0000

Sorry Devils advocate, but the communication in Nature pinpoints different unusual features in this model, other than just packing and correct geometry. One figure shows a solvent exposed part of the molecule which perfectly fits the 2fofc map at 2.5 sigmaa !!! A solvent exposed Trp side chain !!!! at 2.5 sigmaa !!!

By: Sean

Sean — Wed, 16 Dec 2009 01:41:57 +0000

Hi XtalDave,

Exactly, strange indeed

By: Sean

Sean — Wed, 16 Dec 2009 01:38:12 +0000

Hi Jim and welcome!

Good reminder there are certainly other inconsistent features other than just the gaps.

Best wishes with that data set

By: Jim

Jim — Tue, 15 Dec 2009 19:29:46 +0000

Many red flags call into question these structures from Dr. Murthy….. not just large gaps between molecules. For example, the Rosetta team’s analysis of poor atomic packing is significant.

I want to point out from recent experience that gaps in electron density due to one-dimensional disorder, as discussed in that Trame and McKay manuscript that Murthy cites in their C3b reply letter, is seemingly a real phenomenon. In one of our as yet unpublished projects, ~1/3 the a.u. along the c-axis is disordered and the molecular model lattice built (to decent Rfactor/Rfree) is not contiguous along this axis. After much work, the cell and symmetry are correct. Multiple crystallographers have had this diffraction data in hand and no better explanations have been forthcoming.

By: Devils advocate

Devils advocate — Tue, 15 Dec 2009 10:56:01 +0000

Sili: Cheating is worth it only if it’s so much easier than the real thing. C3 wasn’t straightforward at all, but making a plausible model, including crystal contacts, packing, ramachandran statistics etc. and proper noise is a PhD’s amount of work in itself. And being such an unrewarding task, I wouldn’t bother to do it right either.

By: XtalDave

XtalDave — Tue, 15 Dec 2009 08:46:02 +0000

Strange that the apparently “new” crystal form in 2OU1 has EXACTLY the same R-factor after refinement and resolution.

IF one wanted to obsolete a structure and replace it with a better structure (rather than just add an additional pdb entry), you’d imagine that it would have superior resolution or better refinement statistics.

By: Crystal-man

Crystal-man — Mon, 14 Dec 2009 16:57:16 +0000

http://www.proteinscience.org/details/journalArticle/110975/RosettaHoles_Rapid_assessment_of_protein_core_packing_for_structure_prediction_r.html
This publication discusses “gaps” in modeled versus crystal structures. All of the Pdb codes in question are outliers!! using this criteria.