2011-01-19 Blind test data for model-building Updated 2011-06-13, 2013-05-25 This directory contains the raw data for blind tests carried out on the Rosetta+Phaser+Autobuild method for determination of challenging structures by MR and rebuilding with structure-modeling and autobuilding. See the paper "Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization" Frank DiMaio, Thomas C. Terwilliger, Randy J. Read, Alexander Wlodawer, Gustav Oberdorfer, Eugene Valkov, Assaf Alon, Deborah Fass, Herbert L. Axelrod, Debanu Das, Sergey M. Vorobiev, Hideo Iwai, P. Raj Pokkuluri & David Baker (2011) Nature 473, 540-543. Also see: Terwilliger, T. C., DiMaio, F., Read, R. J., Baker, D., Bunkóczi, G., Adams, P. D., Grosse-Kunstleve, R. W., Afonine, P. V., Echols, N. (2012). phenix.mr_rosetta: Molecular replacement and model rebuilding with Phenix and Rosetta. J. Struct. Funct. Genomics 13, 81-90. which describes these tests and all the approaches that were applied to each test case. Some of these could be solved by many methods, and some could be solved only with the use of Rossetta structure-modeling either before molecular replacement or during model-building. Some of the data in the paper are now in this directory; remaining data will be placed here as the models are deposited in the PDB. The subdirectories each contain x-ray data and a starting model, fragments files, and an alignment file. These correspond in most cases to the model after placement by MR. In the work reported in the paper, these models were then used to calculate 2Fo-Fc maps which were input with the models to Rosetta model-building, and the best models were used in autobuilding. In these subdirectories a command file is provided that will run phenix.mr_rosetta to do a similar process (but generating only 20 rosetta models instead of 1000-2000). The structures that could be solved by many methods and those solved only the inclusion of structure-modeling are indicated in the table below, along with the numbering of the blind tests in the paper. (Note: with data as provided in these directories, tests 1-5 (fk4430, bfr258e, niko fj6376, cab55348) and 13 (pc0265) can be solved with phenix.automr/phenix.autobuild.) NOTE: The data in these directories should match the data in the paper, but the models and R-factors will not. The scripts and results in these directories use phenix.mr_rosetta to carry out automatic analysis, while the paper describes the results obtained by Rosetta and phenix.autobuild and making non-automated decisions along the way. Directory Test number in paper PDB ENTRY 12_fk4430 #1 3o8s 2_bfr258e #2 3nng 11_niko #3 4fqd 6_fj6376 #4 3npg 3_cab55348 #5 7_xmrv #6 3nr6 9_thiod #7 3q6o 5_pc02153 #8 10_tirap #9 2y92 4_hp3342 #10 3tx8 13_estan #11 3zyt 1_ag9603a #12 4e2t 8_pc0265 #13 3on5 NOTES: 1. 8_pc0265 data are supplied for solving pc0265 from 2-part template 2. 6_fj6376 pdb entry is listed incorrectly in JSFG paper as 3o8s. It is 3npg. Running phenix.mr_rosetta on this data using the mr_rosetta command files should give good maps in all cases, and nearly-final models in many. Each run of mr_rosetta will give slightly different results. Here are typical values of R/FreeR for the 13 blind cases: 1_ag9603/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.25 / 0.27 2_bfr258e/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.22 / 0.28 3_cab55348/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.19 / 0.23 4_hp3342/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.35 / 0.42 5_pc02153/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.33 / 0.44 6_fj6376/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.25 / 0.30 7_xmrv/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.29 / 0.34 8a_pc0265/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.33 / 0.39 9a_thio/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.24 / 0.30 10_tirap/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.34 / 0.42 11_niko/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.24 / 0.31 12_fk4430/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.25 / 0.29 13_estan/run_2011-01-18/mr_rosetta.logit R/Rfree: 0.21 / 0.25