Software Name Version Classification PHENIX(PHENIX.REFINE: DEV_1769)refinement XDSdata reduction PDB_EXTRACT3.15 data extraction XSCALEdata scaling BALBESphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 2UVDResolution : 1.85→37.46 Å / SU ML : 0.16 / Cross valid method : FREE R-VALUE / σ(F) : 0 / Phase error : 18.3 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.19 3750 4.66 % Rwork 0.154 - - obs 0.156 80438 94.1 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 21.13 Å2 Refinement step Cycle : LAST / Resolution : 1.85→37.46 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6889 0 47 750 7686
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 7049 X-RAY DIFFRACTION f_angle_d0.961 9572 X-RAY DIFFRACTION f_dihedral_angle_d11.92 2444 X-RAY DIFFRACTION f_chiral_restr0.042 1154 X-RAY DIFFRACTION f_plane_restr0.005 1261
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Type 1 1 A4171 X-RAY DIFFRACTION POSITIONAL1 2 B4171 X-RAY DIFFRACTION POSITIONAL1 3 C4171 X-RAY DIFFRACTION POSITIONAL1 4 D4171 X-RAY DIFFRACTION POSITIONAL
LS refinement shell Show large table (7 x 27) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.85-1.8735 0.2607 113 0.1962 2521 X-RAY DIFFRACTION 85 1.8735-1.8981 0.2568 164 0.2072 2567 X-RAY DIFFRACTION 86 1.8981-1.9241 0.2256 127 0.1896 2584 X-RAY DIFFRACTION 87 1.9241-1.9516 0.2545 148 0.1873 2651 X-RAY DIFFRACTION 89 1.9516-1.9807 0.2131 127 0.1814 2668 X-RAY DIFFRACTION 89 1.9807-2.0117 0.2306 132 0.1714 2737 X-RAY DIFFRACTION 90 2.0117-2.0447 0.2005 130 0.1657 2727 X-RAY DIFFRACTION 92 2.0447-2.0799 0.1914 92 0.1635 2812 X-RAY DIFFRACTION 92 2.0799-2.1178 0.202 125 0.1622 2809 X-RAY DIFFRACTION 93 2.1178-2.1585 0.1963 137 0.1605 2813 X-RAY DIFFRACTION 94 2.1585-2.2025 0.2114 129 0.1501 2859 X-RAY DIFFRACTION 94 2.2025-2.2504 0.2154 112 0.1518 2895 X-RAY DIFFRACTION 95 2.2504-2.3028 0.1942 133 0.1472 2846 X-RAY DIFFRACTION 95 2.3028-2.3603 0.1764 138 0.1509 2870 X-RAY DIFFRACTION 95 2.3603-2.4241 0.2104 113 0.1528 2893 X-RAY DIFFRACTION 96 2.4241-2.4955 0.2154 147 0.1477 2883 X-RAY DIFFRACTION 95 2.4955-2.576 0.1831 140 0.15 2899 X-RAY DIFFRACTION 97 2.576-2.668 0.1813 135 0.1492 2949 X-RAY DIFFRACTION 97 2.668-2.7748 0.1884 141 0.1581 2950 X-RAY DIFFRACTION 97 2.7748-2.9011 0.2026 147 0.1568 2909 X-RAY DIFFRACTION 98 2.9011-3.054 0.214 152 0.1535 2989 X-RAY DIFFRACTION 98 3.054-3.2452 0.165 131 0.1528 2943 X-RAY DIFFRACTION 98 3.2452-3.4956 0.1761 186 0.1457 2956 X-RAY DIFFRACTION 98 3.4956-3.8471 0.1727 175 0.133 2989 X-RAY DIFFRACTION 99 3.8471-4.403 0.1773 144 0.1361 2984 X-RAY DIFFRACTION 98 4.403-5.5444 0.1665 170 0.1419 2985 X-RAY DIFFRACTION 99 5.5444-37.47 0.1649 162 0.1706 3000 X-RAY DIFFRACTION 97
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 32) 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 1.7595 0.3159 0.4397 3.1087 -0.4889 3.1765 -0.1071 -0.1338 0.3806 0.0387 0.0565 0.1706 -0.1993 -0.2728 0.0216 0.1657 0.0632 -0.0374 0.1427 -0.0433 0.2334 9.8127 25.8159 17.3389 2 1.1664 -0.1997 -0.1865 4.228 -0.4102 1.4515 0.086 -0.0372 0.1833 0.4378 -0.0259 0.6734 -0.2829 -0.3759 0.1946 0.3535 0.1764 -0.0426 0.3913 -0.2155 0.4926 3.1889 31.5585 23.0724 3 3.6061 3.953 0.1121 8.0256 0.5444 0.8449 -0.0068 -0.2301 0.5202 -0.4473 -0.1349 0.7373 -0.1958 -0.193 0.0869 0.2007 0.0909 -0.0354 0.2549 -0.0288 0.292 1.1036 23.5836 15.6087 4 1.1198 -0.1554 -0.0842 1.1262 -0.2673 0.9544 -0.1064 -0.1132 0.1445 0.1138 0.0427 0.2005 -0.1655 -0.2657 0.0428 0.1322 0.0325 -0.0126 0.1918 -0.0501 0.1993 3.6216 14.2948 17.2148 5 0.6295 0.7853 -0.7195 3.9224 -3.5251 5.2853 0.0269 -0.017 0.0407 0.0473 -0.0021 0.2381 -0.1841 -0.2265 -0.0403 0.0827 0.0262 -0.0222 0.1855 -0.0248 0.2063 4.5614 8.8528 13.0546 6 0.557 0.0603 0.2909 1.5275 -1.4024 4.4302 0.0187 -0.0202 0.0128 0.0798 -0.0023 0.1128 -0.1015 -0.0229 -0.0251 0.0506 0.0066 0.0035 0.0963 -0.0028 0.1063 14.3861 6.7755 17.8634 7 1.2332 0.3757 1.1509 1.2096 0.2531 1.8132 0.0652 -0.1516 0.0705 0.134 -0.0683 0.1175 -0.0122 -0.2563 -0.0249 0.112 0.002 0.0093 0.1371 -0.0222 0.1308 19.2774 14.7179 24.0973 8 1.7638 0.1103 0.5487 0.7371 -0.2297 8.462 0.018 -0.0401 0.0345 0.0674 -0.0057 -0.0183 -0.0092 -0.1507 -0.0495 0.0724 -0.0122 -0.0112 0.0764 -0.0212 0.1156 24.5171 11.1526 18.2872 9 1.7928 -0.0579 -1.0845 3.5991 -0.4149 2.0691 0.0359 0.0817 -0.5489 0.0356 0.013 0.1787 0.3653 -0.288 -0.0518 0.2238 -0.0977 -0.0073 0.1656 0.0003 0.2743 9.9261 -25.8643 18.4081 10 2.2447 -2.1037 -0.9975 2.3018 0.3874 1.3554 0.1597 0.2469 -0.7548 -0.8362 0.0819 0.7351 0.509 -0.5831 -0.1476 0.4621 -0.2226 -0.0463 0.3723 -0.076 0.4959 4.2726 -31.8615 12.0515 11 2.8373 -2.2758 0.386 2.2625 0.2213 1.3504 -0.1644 -0.0135 -0.6672 0.4119 0.1183 0.8018 0.3667 -0.5414 0.0334 0.2618 -0.1436 0.062 0.363 -0.0217 0.3601 1.0667 -23.7148 19.329 12 1.1227 0.4658 0.0411 1.1889 -0.0628 0.5546 -0.0479 -0.0649 -0.2062 -0.0603 0.0396 0.2036 0.2808 -0.4431 -0.0089 0.1737 -0.0718 0.0312 0.2534 -0.0227 0.245 3.6387 -14.4029 17.9797 13 1.7001 -1.1503 0.9773 4.1748 -3.2942 4.5867 0.0437 -0.1386 -0.1077 0.1487 0.0314 0.3806 0.0572 -0.2852 -0.1095 0.1145 -0.0528 0.0195 0.2172 -0.015 0.1977 4.0165 -8.8575 21.8938 14 1.2525 0.7287 -1.2799 3.8512 -3.9049 6.9091 -0.0227 -0.0613 -0.0641 -0.085 -0.0809 -0.0168 0.2511 -0.0053 0.1341 0.0977 -0.0028 0.0009 0.1041 -0.0118 0.1036 15.7235 -8.5889 15.7502 15 1.5354 -0.8267 -0.1945 1.7827 -0.4314 0.943 -0.0011 -0.1625 -0.0601 0.1009 0.0493 0.1915 0.1446 -0.0338 -0.0556 0.0886 -0.0338 0.0125 0.1038 -0.0023 0.1218 14.587 -7.771 23.3467 16 4.6687 -4.085 1.7976 4.9765 -3.2487 5.6099 0.4508 0.6132 0.0038 -0.5824 -0.3105 0.4046 0.0758 -1.2359 -0.0456 0.3072 0.0653 -0.042 0.4204 -0.0928 0.2168 17.7378 -10.0928 -0.5362 17 1.616 -0.0119 -0.8675 1.1277 0.1296 5.1478 0.0215 0.0287 -0.0673 -0.0493 -0.0023 0.0517 0.1998 -0.2217 -0.0182 0.0754 0.0078 -0.0018 0.0804 0.0007 0.1142 23.3367 -15.7184 15.0783 18 2.0164 -0.5949 0.2172 1.4404 -0.7146 2.2143 0.0311 -0.0418 -0.0942 0.0366 -0.0102 -0.0382 0.1858 0.1315 -0.0285 0.1571 0.0348 0.0048 0.082 0.0134 0.1017 44.0989 -27.0465 25.0461 19 1.7216 2.297 -0.6032 6.3505 -1.4022 1.3649 -0.079 0.0584 -0.2563 0.0327 -0.0124 -0.7259 0.2277 0.2403 0.0526 0.1873 0.0633 0.0033 0.1485 0.0215 0.1443 51.5562 -23.4292 21.8935 20 0.7451 -0.4453 -0.0692 3.0063 1.352 1.2847 -0.0051 0.0449 -0.0309 0.1129 0.0281 -0.1664 0.1633 0.1949 -0.0327 0.1137 0.0166 -0.0019 0.1391 0.0341 0.1076 48.5379 -11.9326 19.3358 21 1.2306 -1.456 -1.519 1.7538 2.1752 5.276 -0.0505 0.0441 -0.0439 0.189 -0.1066 0.166 0.1651 -0.0456 0.157 0.0952 -0.0283 0.0016 0.1006 0.0204 0.0999 36.562 -8.7601 22.2717 22 0.7009 0.3739 0.3118 1.1078 1.0003 1.405 0.0203 0.0735 -0.0401 0.0265 -0.0141 -0.0208 0.1242 0.0657 -0.0011 0.0987 0.014 -0.0044 0.0799 0.0125 0.0902 37.8018 -8.4558 15.2372 23 5.75 3.3317 1.7375 6.5346 1.9814 7.3854 0.3181 -0.6337 0.4578 1.0198 -0.2578 -0.3175 -0.3734 0.6554 -0.089 0.4151 -0.0952 -0.021 0.3666 -0.003 0.2679 35.3038 -7.2821 39.8863 24 1.2391 -0.606 -0.5884 1.5978 0.4299 3.265 -0.0278 -0.0328 -0.0311 0.1543 0.0095 0.039 0.1218 -0.036 0.0219 0.0885 -0.0211 -0.0013 0.0766 0.0133 0.1052 28.9798 -14.8345 24.362 25 4.0842 0.5259 0.701 2.1142 -1.3778 3.4923 0.0369 -0.1259 0.2908 0.1027 0.0192 -0.0591 -0.2257 0.0706 -0.0881 0.1308 -0.0663 -0.0229 0.0697 0.0281 0.1055 41.6725 25.8297 18.3658 26 2.3202 -0.2259 -0.5376 1.7717 -0.0632 2.761 -0.0213 0.0484 0.0837 0.0174 0.0221 -0.0499 -0.1636 0.1806 0.009 0.1666 -0.041 -0.0137 0.1033 0.0142 0.1164 45.6906 27.2058 11.6438 27 3.0015 -2.6511 0.9597 7.1105 -1.6453 1.7885 -0.0771 -0.071 0.1594 0.2683 0.0499 -0.5687 -0.1982 0.2416 0.0112 0.1657 -0.0718 -0.0126 0.1698 0.0152 0.1101 51.5912 23.5169 17.4457 28 1.0056 0.3333 -0.0379 2.1967 0.1433 0.4014 -0.0109 -0.0469 0.0532 -0.1438 -0.0162 -0.1245 -0.2107 0.1498 0.0178 0.1329 -0.0286 0.0009 0.1479 0.0314 0.0917 48.8069 14.2741 17.5608 29 0.707 -0.1003 -0.1181 1.1461 0.6604 1.5239 0.0258 -0.0334 0.0036 0.0212 -0.0542 -0.0401 -0.063 0.0407 0.0179 0.0983 -0.0102 -0.006 0.0852 0.0195 0.088 41.2372 8.83 20.9927 30 7.6346 2.4413 1.2378 6.3281 -1.1787 3.1898 0.1313 0.6507 -0.5305 -0.6788 -0.2291 -0.4532 0.361 0.7268 -0.0051 0.3649 0.0698 -0.004 0.311 0.0047 0.2297 37.59 7.2989 -1.9687 31 1.2551 0.4563 0.5084 1.326 0.8747 4.6832 0.0584 0.0759 0.0086 -0.118 0.0335 -0.0453 -0.147 -0.0651 -0.052 0.1104 0.0053 -0.0015 0.0677 0.0112 0.1043 30.6468 18.0425 9.8194 32 2.0136 0.2351 0.7678 0.0879 -0.346 5.4506 0.0244 -0.0535 -0.0264 -0.016 -0.0075 0.0272 -0.0556 -0.061 -0.0257 0.0745 0.0109 -0.0055 0.0574 0.0096 0.0963 27.8707 11.0362 17.1461
Refinement TLS group Show large table (4 x 32) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 CHAIN 'A' AND (RESID 3 THROUGH 40 )2 X-RAY DIFFRACTION 2 CHAIN 'A' AND (RESID 41 THROUGH 54 )3 X-RAY DIFFRACTION 3 CHAIN 'A' AND (RESID 55 THROUGH 67 )4 X-RAY DIFFRACTION 4 CHAIN 'A' AND (RESID 68 THROUGH 104 )5 X-RAY DIFFRACTION 5 CHAIN 'A' AND (RESID 105 THROUGH 133 )6 X-RAY DIFFRACTION 6 CHAIN 'A' AND (RESID 134 THROUGH 173 )7 X-RAY DIFFRACTION 7 CHAIN 'A' AND (RESID 174 THROUGH 240 )8 X-RAY DIFFRACTION 8 CHAIN 'A' AND (RESID 241 THROUGH 258 )9 X-RAY DIFFRACTION 9 CHAIN 'B' AND (RESID 3 THROUGH 40 )10 X-RAY DIFFRACTION 10 CHAIN 'B' AND (RESID 41 THROUGH 54 )11 X-RAY DIFFRACTION 11 CHAIN 'B' AND (RESID 55 THROUGH 67 )12 X-RAY DIFFRACTION 12 CHAIN 'B' AND (RESID 68 THROUGH 104 )13 X-RAY DIFFRACTION 13 CHAIN 'B' AND (RESID 105 THROUGH 133 )14 X-RAY DIFFRACTION 14 CHAIN 'B' AND (RESID 134 THROUGH 153 )15 X-RAY DIFFRACTION 15 CHAIN 'B' AND (RESID 154 THROUGH 186 )16 X-RAY DIFFRACTION 16 CHAIN 'B'