On Mon, Jul 22, 2013 at 10:19 AM, Stefan Gajewski <[email protected]>wrote:
> The maps shows signs of over fitting, the B-factors do not look correct in > my opinion. What do "correct" B-factors look like? What refinement strategy did you use for them? > Note that the R-free value in the 3.4A shell is lower than the R-work (and > also the Rpim in that shell!) which clearly indicates this refinement was > not stable. > I don't think it indicates anything about the "stability" of refinement - my guess would be that the NCS is biasing R-free. I suppose it could also indicate that the data in the 3.6-3.4 range are basically noise, although if the maps look better then that would suggest the opposite. > The structure contains no beta sheets and refinement also profits greatly > from very rigid high-order NCS. The maps are very detailed, in fact better > than some 2.8A maps I've seen before. The 0.2A in question here are > actually quite helpful to increase the map quality, so I keep wondering if > I should deposit the structure with them or keep them only for my own > interpretation. > I would deposit the data to 3.4Å in any case; what cutoff you refine the structure to is a separate decision. Before I continue optimizing the integration/refinement I would like to > hear suggestions from the experts where to make the resolution cut-off in > this case? > Do I have all information I need to make that decision? > What arguments should I present when dealing with the reviewers? I mean, > the Rrim/Rmerge values are really very high. > Do what Karplus & Diederichs suggest: take the structure refined to 3.4Å, and recalculate the R-factors for that model with the data cut to 3.6Å. If the R-free calculated this way is below the R-free for the model refined to only 3.6Å, then the extra 0.2Å is contributing real information and improving the quality of your model, which is the best justification for extending to higher resolution. -Nat
