Software Name Version Classification PHENIX(1.10.1_2155: ???)refinement XDSdata reduction XDSdata scaling PHENIXphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 2j9xResolution : 1.972→47.255 Å / SU ML : 0.25 / Cross valid method : FREE R-VALUE / σ(F) : 1.35 / Phase error : 25.1 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.232 4057 5 % Rwork 0.1784 - - obs 0.1811 81129 96.57 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 1.972→47.255 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 9516 0 53 398 9967
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 9715 X-RAY DIFFRACTION f_angle_d0.851 13182 X-RAY DIFFRACTION f_dihedral_angle_d14.636 5845 X-RAY DIFFRACTION f_chiral_restr0.051 1517 X-RAY DIFFRACTION f_plane_restr0.006 1726
LS refinement shell Show large table (7 x 29) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.9715-1.9947 0.3852 84 0.341 1601 X-RAY DIFFRACTION 58 1.9947-2.0191 0.3545 128 0.2894 2422 X-RAY DIFFRACTION 89 2.0191-2.0446 0.3189 140 0.264 2660 X-RAY DIFFRACTION 95 2.0446-2.0715 0.2878 141 0.2311 2696 X-RAY DIFFRACTION 99 2.0715-2.0999 0.2646 144 0.216 2726 X-RAY DIFFRACTION 99 2.0999-2.1299 0.3028 143 0.2082 2727 X-RAY DIFFRACTION 99 2.1299-2.1617 0.2846 143 0.2143 2715 X-RAY DIFFRACTION 99 2.1617-2.1955 0.2617 144 0.2097 2735 X-RAY DIFFRACTION 99 2.1955-2.2315 0.2697 145 0.2051 2757 X-RAY DIFFRACTION 99 2.2315-2.2699 0.2691 141 0.218 2679 X-RAY DIFFRACTION 99 2.2699-2.3112 0.2754 145 0.2038 2739 X-RAY DIFFRACTION 99 2.3112-2.3557 0.2774 143 0.2069 2725 X-RAY DIFFRACTION 99 2.3557-2.4037 0.2497 144 0.1998 2726 X-RAY DIFFRACTION 99 2.4037-2.456 0.2524 142 0.2049 2707 X-RAY DIFFRACTION 99 2.456-2.5131 0.2541 145 0.196 2746 X-RAY DIFFRACTION 99 2.5131-2.576 0.2891 141 0.1993 2693 X-RAY DIFFRACTION 99 2.576-2.6456 0.2383 143 0.2004 2719 X-RAY DIFFRACTION 99 2.6456-2.7235 0.2639 143 0.1983 2705 X-RAY DIFFRACTION 98 2.7235-2.8114 0.2516 138 0.2019 2619 X-RAY DIFFRACTION 96 2.8114-2.9118 0.2554 135 0.2023 2566 X-RAY DIFFRACTION 93 2.9118-3.0284 0.27 142 0.1941 2696 X-RAY DIFFRACTION 98 3.0284-3.1662 0.2381 144 0.1887 2738 X-RAY DIFFRACTION 99 3.1662-3.3331 0.2748 142 0.178 2699 X-RAY DIFFRACTION 98 3.3331-3.5418 0.1843 144 0.1681 2742 X-RAY DIFFRACTION 99 3.5418-3.8152 0.181 142 0.1538 2688 X-RAY DIFFRACTION 98 3.8152-4.1989 0.1959 142 0.1438 2710 X-RAY DIFFRACTION 98 4.1989-4.806 0.1748 142 0.1308 2701 X-RAY DIFFRACTION 97 4.806-6.0531 0.2313 140 0.1647 2655 X-RAY DIFFRACTION 96 6.0531-47.2684 0.2121 147 0.1642 2780 X-RAY DIFFRACTION 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 21) Hide large table ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 3.9935 -1.9349 0.9301 8.6584 -3.0223 3.2431 -0.0989 -0.4838 -0.3922 0.4395 0.1255 0.4384 0.1072 -0.1597 -0.0553 0.2491 -0.019 0.0767 0.2598 0.0144 0.2593 -3.6851 47.3009 101.2201 2 3.8949 1.0824 0.5843 4.4373 -1.3553 3.1242 0.0865 -0.2942 -0.0805 0.4383 -0.0947 -0.0818 -0.3105 0.0334 0.0014 0.2928 0.0227 0.0014 0.2067 -0.0143 0.2285 1.293 60.1854 99.0374 3 2.9663 1.6975 -0.8672 3.0439 0.7386 7.4758 0.0495 -0.4143 -0.0981 0.5161 -0.2885 -0.3608 0.0881 0.5213 0.2496 0.4178 0.0682 -0.1676 0.3931 0.0619 0.3581 14.1809 55.1899 101.4119 4 5.3331 -0.2766 -1.7493 4.2657 -0.2373 3.0936 0.1162 0.3795 -0.1828 -0.224 -0.3935 -0.4833 0.5429 0.686 0.2331 0.411 0.1632 0.0324 0.3799 0.0596 0.4632 12.9824 45.9854 92.5575 5 6.3549 -2.0464 0.0966 2.2875 -1.242 4.3237 0.1395 0.3249 -0.2659 -0.5226 -0.0964 0.4959 0.4745 -0.0553 -0.0634 0.3891 0.0067 -0.0658 0.2606 0.0036 0.4024 -5.3969 42.2981 89.697 6 0.8633 0.5827 -0.5341 1.4529 -0.9443 1.5685 -0.0612 -0.1661 -0.2122 0.1186 -0.1337 -0.4758 -0.0153 0.2704 0.22 0.1694 -0.0058 -0.0488 0.2983 0.0062 0.3274 27.4605 75.8249 74.6345 7 7.3475 -0.2304 -3.019 3.4474 0.2029 5.6857 0.0257 0.2917 0.0678 -0.2135 0.0637 0.1702 -0.2575 -0.3301 -0.1005 0.1779 -0.0147 -0.0385 0.1835 0.0027 0.2047 11.1034 69.281 67.6948 8 3.8352 3.4489 -0.0116 5.5134 -0.7561 1.6136 0.0013 -0.1019 -0.2815 0.023 -0.0511 -0.4215 -0.0124 0.2154 0.043 0.1518 0.0282 -0.0311 0.248 0.0297 0.236 23.0477 71.9144 77.6797 9 0.9255 0.7352 -1.1679 2.6726 -2.0013 2.8541 0.2138 -0.1111 0.0836 0.4667 -0.0519 0.0564 -0.4142 0.0505 -0.1707 0.2962 -0.0278 -0.0165 0.2812 -0.0527 0.2111 16.8624 87.9861 82.1255 10 2.6263 0.9085 -1.1545 6.2628 -2.366 3.2783 -0.0972 0.6241 0.3995 -0.1722 0.2008 0.3226 -0.1802 -0.1188 -0.0753 0.3073 -0.0994 -0.061 0.4765 0.1041 0.4031 2.9907 115.47 18.7591 11 3.1016 -3.0968 -1.0302 7.269 -2.9181 4.5401 0.302 0.5027 0.2523 -0.5237 -0.491 -0.1171 0.6476 -0.0091 0.1662 0.3832 -0.1182 0.0122 0.589 0.0512 0.2506 15.18 106.3794 17.3012 12 3.7418 1.2903 2.8245 7.2994 5.6767 7.1344 -0.0751 0.7649 0.3727 -0.5271 0.276 -0.3761 -0.4868 0.7377 -0.2824 0.3248 -0.1073 0.044 0.5549 0.0912 0.364 20.6723 114.3156 18.9292 13 6.4388 -3.3501 1.275 3.0581 -2.1647 8.3339 -0.0554 0.2172 -0.0118 0.0763 0.1019 -0.4925 -0.2873 0.6101 0.0022 0.4263 -0.2222 0.004 0.5887 0.1145 0.6619 22.7651 121.0017 24.4814 14 3.9528 -2.3969 -0.0328 3.1737 -0.311 4.9246 0.0651 -0.2023 0.5068 0.4203 -0.0915 0.0128 -0.5257 -0.1998 -0.0852 0.4514 -0.0609 -0.0295 0.357 0.1241 0.6004 3.362 125.146 28.061 15 0.8524 0.0927 -0.4985 2.2746 -1.2748 1.833 -0.1734 -0.0028 -0.0484 -0.0875 0.0236 -0.2698 0.0745 0.0315 0.1497 0.1631 -0.0454 0.0083 0.2507 -0.0599 0.2718 29.5946 94.0576 48.2869 16 7.5485 2.2402 1.8188 4.4407 -0.0356 4.6625 -0.0239 -0.0978 -0.076 -0.1829 0.0715 0.1267 0.1869 -0.2827 -0.042 0.1717 0.0428 0.0205 0.2184 -0.0049 0.1799 11.9512 100.4579 51.8314 17 7.2057 -1.8751 -2.6006 3.5276 0.0434 5.3153 0.0235 0.1511 0.4469 -0.0815 0.1469 0.0072 -0.2631 -0.2917 -0.1725 0.2054 -0.0248 -0.0001 0.2302 0.0132 0.231 17.7828 106.1828 42.2133 18 5.921 -5.4092 0.754 8.0436 -1.6325 3.1536 -0.4159 -0.2505 0.0079 -0.1295 -0.0063 -0.9905 0.2455 0.3811 0.3858 0.2232 -0.0198 0.1136 0.2608 0.0053 0.4359 35.0813 88.5765 47.0257 19 1.0663 -0.7377 -1.1884 4.0549 -0.9174 2.6257 -0.5973 0.6005 -0.1723 -1.2793 0.3674 -0.4231 0.6588 -0.2573 -0.0409 0.7041 -0.139 0.1849 0.3388 -0.068 0.2678 26.9065 81.8914 37.857 20 0.4168 -1.2921 0.9314 4.656 -2.4203 3.8636 -0.025 0.199 -0.2646 -0.6913 0.2773 0.3995 0.5201 -0.8471 -0.2311 0.5277 -0.2135 -0.0003 0.4909 -0.0642 0.3123 17.8569 91.2843 31.0031 21 0.5579 0.184 0.5164 2.6325 -0.46 4.4194 -0.2725 0.2163 -0.3205 -0.8056 0.165 0.0166 0.6547 -0.443 0.1496 0.5987 -0.1965 0.0744 0.357 -0.0919 0.3252 20.1029 74.7284 45.6046
Refinement TLS group Show large table (4 x 21) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 42 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 43 through 136 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 137 through 159 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 160 through 216 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 217 through 269 )6 X-RAY DIFFRACTION 6 chain 'B' and (resid 1 through 96 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 97 through 160 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 161 through 215 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 216 through 383 )10 X-RAY DIFFRACTION 10 chain 'C' and (resid 2 through 102 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 103 through 136 )12 X-RAY DIFFRACTION 12 chain 'C' and (resid 137 through 159 )13 X-RAY DIFFRACTION 13 chain 'C' and (resid 160 through 177 )14 X-RAY DIFFRACTION 14 chain 'C' and (resid 178 through 261 )15 X-RAY DIFFRACTION 15 chain 'D' and (resid 1 through 95 )16 X-RAY DIFFRACTION 16 chain 'D'