Hi Wolfram, We recently moved pdb-redo to a new domain, so the entry you are interested in is at https://pdb-redo.eu/db/2h58 This entry at 1.85A resolution was indeed refined with anisotropic B-factors based on the Hamilton R ratio test. There was no paired refinement for this entry. We only do that if the deposited data extends to a resolution higher than what was used in the refinement of the PDB entry. Of course you can use our server to do paired refinement for your dataset. It works best when your model is already in a good state.
Cheers, Robbie Sent from my Windows 10 phone Van: wtempel<mailto:[email protected]> Verzonden: vrijdag 2 juni 2017 22:44 Aan: [email protected]<mailto:[email protected]> Onderwerp: [ccp4bb] Refining a crystal structure with (very) high solvent content 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. 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
