On 6/2/2017 1:42 PM, wtempel wrote: > Hello all, > crystals with high solvent content tend to diffract poorly, at least > according to intuition. Several years ago we solved a structure > <http://www.rcsb.org/pdb/explore/explore.do?structureId=2h58> that > appeared to buck that trend with a solvent content of ≈0.8 and > resolution beyond 2 Å, per merging statistics and visibility of spots on > diffraction images. > I would welcome my colleagues’ opinions as to why I might observe the > following: > > 1. Paired refinement (similar to Fig. 1 in Karplus&Diederichs > <http://doi.org10.1126/science.1218231>) indicates that adding any > higher resolution data beyond 3.4 Å, the lowest high resolution > cut-off limit I tried, does not improve R-factors at the common > lower resolution cutoff. Yes, diffraction is anisotropic in this > case, but seemingly not to that extent. I hesitate to “throw out” > all data beyond 3.4 Å, or whatever lower resolution cut-off I might try. > 2. The Fo-Fc map, when countoured at ± 3 rmsd, includes many more > (uninterpretable) features than I would expect after refinement to > residuals in the mid-to-lower twenties. For expected map appearance, > I had to crank up the coutour level to > 5 rmsd, like in the > attached screenshot of the ADP·Mg^++ omit map.
This is one of the prime examples of the failure of describing contour levels in terms of "sigma". First, the number you are using is not a "standard deviation" or any other measure of the error level of the map but is simply the rms value of the map. If you calculate the rms of a difference map where 80% of the unit cell is bulk solvent, and therefore flat, you will, of course, get a much smaller number than if the unit cell contained 80% protein with all the the expected difference map features that come from a model with an R value of ~20%. Then when you contour at three times this absurdly small number you will see all sorts of features you are not used to seeing. Selecting a contour level based on the e/A^3 is much less sensitive to the amount of solvent in the crystal is gives much more consistent results. Dale Tronrud > > Could these observations be linked to the high solvent content? (1) A > high solvent content structure has a higher-than-average > observation-to-parameter ratio, sufficiently high even when limited to > stronger, low-resolution reflections? (2) Map normalization may not be > attuned to such high solvent content? > I am interested in analyzing the automated decision-making of the > PDB-REDO of this entry <http://www.cmbi.ru.nl/pdb_redo/h5/2h58>, such as > paired refinement results and selection of ADP model. Should I find this > information in the “All files (compressed)” archive > <http://www.cmbi.ru.nl/pdb_redo/cgi-bin/zipper.pl?id=2h58>? The “fully > optimized structure’ > <http://www.cmbi.ru.nl/pdb_redo/h5/2h58/2h58_final.pdb> shows |ANISOU| > cards and |NUMBER OF TLS GROUPS : NULL|. Does this mean that individual > ADPs have been refined anisotropically? > Looking forward to your insights, > Wolfram Tempel > >
