Software Name Version Classification NB XSCALEdata scalingShow PHASER2.5.0phasingShow PHENIX1.8_1069refinementShow PDB_EXTRACT3.11 data extractionShow XDSdata scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 3U7WResolution : 1.65→37.888 Å / Occupancy max : 1 / Occupancy min : 0.19 / FOM work R set : 0.8742 / SU ML : 0.13 / σ(F) : 1.35 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.2034 1826 1.71 % RANDOM Rwork 0.1738 - - - obs 0.1744 106921 99.38 % - all - 107588 - -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 94.88 Å2 / Biso mean : 25.5521 Å2 / Biso min : 7.09 Å2 Refinement step Cycle : LAST / Resolution : 1.65→37.888 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6606 0 80 911 7597
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 6862 X-RAY DIFFRACTION f_angle_d1.184 9306 X-RAY DIFFRACTION f_chiral_restr0.076 1021 X-RAY DIFFRACTION f_plane_restr0.006 1181 X-RAY DIFFRACTION f_dihedral_angle_d13.785 2478
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 13
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.65-1.6946 0.259 138 0.2176 8010 8148 99 1.6946-1.7445 0.2514 139 0.2077 7940 8079 99 1.7445-1.8008 0.2371 138 0.1974 7978 8116 99 1.8008-1.8651 0.2345 139 0.1901 8002 8141 100 1.8651-1.9398 0.2517 139 0.1851 8003 8142 100 1.9398-2.0281 0.2548 139 0.1828 8002 8141 100 2.0281-2.135 0.1825 140 0.1791 8035 8175 99 2.135-2.2688 0.2082 140 0.1748 8073 8213 100 2.2688-2.4439 0.1949 141 0.1736 8110 8251 100 2.4439-2.6898 0.2144 141 0.174 8115 8256 100 2.6898-3.0789 0.1969 142 0.1722 8131 8273 99 3.0789-3.8784 0.1869 143 0.1524 8242 8385 100 3.8784-37.8982 0.1786 147 0.1707 8454 8601 98
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 33) 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 0.909 -0.0011 0.2097 0.9337 -0.2182 1.9303 0.016 -0.0429 -0.0886 -0.0335 -0.0141 0.0485 0.1352 -0.0191 0.0145 0.0999 0.0067 -0.0023 0.1198 0.0041 0.1436 20.0634 12.1811 32.2555 2 0.8514 -0.1228 0.3471 0.914 -0.0677 0.9051 0.0356 0.0066 0.0378 -0.0431 -0.0123 -0.0645 -0.1195 -0.0648 -0.0228 0.1305 0.0078 -0.0071 0.1165 0.0069 0.1474 19.8903 22.3451 25.2908 3 0.8457 -0.1083 0.3745 0.211 -0.2834 0.8977 0.0225 0.0172 0.0084 -0.0423 0.0071 -0.0022 -0.0606 -0.023 -0.0284 0.0834 0.0022 0.0088 0.068 0.0013 0.0823 15.9807 20.1269 25.555 4 0.0909 -0.1142 0.2618 0.7511 -0.1734 1.2926 0.1996 -0.2734 -0.1874 0.2764 -0.2401 -0.0181 0.0509 0.0617 0.0793 0.1571 0.0091 0.0168 0.3275 0.0389 0.1931 1.9217 3.0233 54.263 5 1.4237 0.897 0.2312 1.0479 -0.2929 1.1158 0.0558 -0.1846 -0.1261 -0.0829 -0.1336 -0.0221 0.1487 0.1267 0.0959 0.1446 0.0241 0.0096 0.2286 -0.0031 0.1888 -1.9061 1.6224 47.5258 6 5.7906 1.8896 -2.9099 2.0682 -1.5888 3.057 -0.0354 -0.6138 -0.2266 0.0631 -0.1301 0.0749 0.3906 0.1594 0.0162 0.2793 0.0229 0.0015 0.3442 0.0835 0.3498 -4.0569 -7.2164 55.4692 7 1.4466 0.3315 0.1186 1.5947 0.1995 1.8296 0.0446 -0.1824 0.2458 0.125 0.0264 0.1533 -0.1463 -0.1469 -0.0706 0.1551 0.0265 0.0032 0.152 0.0062 0.195 -8.0407 27.3468 27.9621 8 1.7015 -0.3276 -0.0362 1.3647 -0.1244 1.5672 0.0304 -0.0136 0.3146 -0.0924 0.0039 -0.0332 -0.3568 0.0138 -0.0181 0.2199 0.005 -0.0002 0.1669 0.0142 0.2194 1.0826 31.8156 21.4588 9 1.1974 0.5809 -0.9745 2.6542 -2.4248 2.5581 0.1143 -0.0426 -0.5045 -0.2185 0.1233 0.2308 0.4881 -0.031 -0.0715 0.1785 0.0089 -0.0054 0.1868 0.0271 0.1892 1.9549 15.3764 24.4611 10 2.1029 1.0066 -0.2523 0.9386 -0.7343 1.5672 -0.0327 0.2568 -0.0469 -0.1099 0.0157 -0.0419 -0.1533 -0.1481 -0.0262 0.1612 0.0076 -0.0155 0.2101 0.0297 0.2038 -2.4116 26.1339 14.928 11 2.8829 0.8395 -0.2258 0.6717 -0.2696 0.955 -0.0244 0.0248 -0.0307 -0.0423 0.0659 0.0402 -0.0715 -0.0709 -0.0276 0.1478 0.0105 0.0016 0.1365 0.0137 0.1525 -1.2209 23.6384 24.3304 12 2.8126 1.8172 -2.5898 1.1258 -1.7248 2.3095 0.0542 0.2031 0.2577 0.0208 0.1134 0.0689 -0.074 -0.2852 -0.0604 0.1276 0.0101 -0.0113 0.2116 0.0377 0.1649 -15.449 18.2141 34.1529 13 1.0733 -0.1776 0.2442 0.9306 -0.3444 2.1641 -0.0228 -0.0482 0.024 0.0027 -0.069 -0.067 0.04 0.2621 0.0832 0.1299 -0.0049 -0.007 0.2066 0.0117 0.1522 -8.8134 10.5887 54.6745 14 0.4283 -0.2877 -0.785 0.1761 0.22 1.8303 0.0358 -0.0056 0.1454 -0.0459 0.0015 0.0384 -0.2196 0.1864 0.0052 0.1967 -0.0403 -0.0086 0.1938 -0.0134 0.1818 -6.7196 19.1069 59.8685 15 0.6225 0.0621 -0.0462 0.5255 -0.5535 2.4072 -0.0522 -0.0399 0.064 0.0357 -0.0421 -0.0036 -0.0436 0.286 0.075 0.1286 -0.0056 -0.0093 0.1721 -0.0032 0.1508 -8.3988 12.0616 54.6593 16 1.3158 -0.0609 0.0171 0.7018 -0.1604 2.2997 -0.0593 0.0007 0.1351 0.0628 -0.0354 -0.0261 -0.0893 -0.2673 -0.0061 0.1415 0.0112 -0.0069 0.1718 -0.0151 0.1509 -18.3888 13.6305 56.9393 17 0.5392 -0.2319 -0.5276 1.3932 -0.5038 1.4705 0.0658 0.0415 -0.0627 -0.1682 -0.1109 -0.1139 0.133 0.1579 0.0127 0.1856 0.0339 -0.0052 0.1342 0.0105 0.169 -22.2521 -30.1258 32.1685 18 1.1426 -0.4398 -0.63 1.4151 -0.3169 1.3011 0.0667 0.0011 0.0197 -0.0997 -0.0672 -0.1144 0.0726 0.1283 -0.0126 0.1797 0.0183 -0.0079 0.1302 0.0198 0.1561 -23.7037 -26.199 33.2554 19 1.364 0.437 -0.3123 0.5529 0.1137 0.7185 -0.1306 -0.4322 0.0879 0.3945 0.0569 -0.0682 0.2967 0.4556 0.089 0.4126 0.1398 0.062 0.319 -0.0257 0.2917 -4.4495 -15.9158 5.7429 20 1.3676 -1.1163 -0.9724 0.9843 0.1922 1.6797 -0.2432 -0.358 0.0855 0.288 0.2083 -0.2564 0.4613 0.542 0.0562 0.3162 0.1356 -0.0281 0.3335 -0.0212 0.2496 -5.4687 -10.7054 11.8719 21 1.2104 0.0004 -0.4379 2.7634 0.8628 1.7735 -0.1811 -0.1372 0.2291 0.4024 0.5033 -0.479 0.2299 0.5849 -0.091 0.2711 0.1044 -0.066 0.3726 -0.1036 0.3745 -0.1298 -5.8641 10.796 22 0.9998 -0.2776 0.5851 8.0681 -2.865 1.7354 -0.1092 0.3951 -0.3217 0.357 0.105 -0.9441 0.5857 0.9422 0.0187 0.3897 0.1922 -0.0214 0.5319 -0.1623 0.5326 5.487 -11.9545 8.1067 23 0.7942 0.5877 0.1031 0.8751 -0.0579 1.1798 -0.0171 0.0404 -0.0642 -0.1987 0.1352 0.1084 0.124 -0.1119 -0.1041 0.1899 -0.0114 -0.034 0.1399 0.0258 0.1794 -32.2286 -4.2482 27.7717 24 1.4872 1.054 -0.5258 1.7428 -0.4667 0.3369 -0.0873 0.1031 0.1005 -0.2062 0.1088 0.0552 0.0604 -0.1634 0.0072 0.1676 -0.0155 -0.0148 0.1456 0.0084 0.1496 -36.5372 -11.4751 33.9932 25 2.9081 0.3685 -1.9584 1.3513 -0.7064 1.6368 0.0864 -0.3347 0.5673 0.0993 0.1906 -0.5706 0.2497 0.6327 -0.0258 0.1446 -0.0114 0.0349 0.1708 -0.0014 0.2819 -19.847 -11.8754 33.7313 26 0.6235 0.2371 -0.2006 1.7894 -0.0389 0.9479 0.0299 -0.0441 0.0475 0.0258 -0.0327 0.0105 -0.022 -0.06 -0.0029 0.1403 0.0019 -0.0076 0.1317 0.0111 0.1502 -30.0612 -8.022 36.7568 27 0.9118 0.9867 -0.8809 1.6234 -0.9423 0.7229 -0.02 0.0551 -0.01 -0.0409 0.0348 -0.0458 0.0373 -0.0515 -0.0328 0.1644 0.006 0.0144 0.1418 0.0122 0.1614 -22.0208 4.5862 21.9832 28 1.6586 -0.9279 -0.1556 4.0381 1.1016 1.8021 0.0798 0.2094 0.1711 -0.131 0.1685 -0.8789 0.2487 0.5328 0.0058 0.2675 0.0782 0.043 0.2963 -0.018 0.2321 -5.4408 -6.6523 -1.9365 29 0.5263 -0.2013 -0.77 1.4351 1.5759 3.3412 0.0131 0.0186 0.0098 -0.012 0.073 -0.0129 0.2321 -0.0133 -0.0177 0.196 0.0051 0.004 0.1474 0.0049 0.1574 -17.5164 -1.2585 5.9997 30 0.2532 -0.26 0.5861 0.4584 -0.8478 2.6095 0.09 -0.028 -0.1012 -0.0929 0.1573 0.287 0.2422 -0.3298 -0.0879 0.2499 -0.0343 -0.0207 0.2047 0.0303 0.2127 -20.7466 -7.3126 -1.871 31 1.803 -0.2611 -0.0633 4.1522 1.1186 3.184 -0.2525 -0.3858 0.0955 0.3795 0.4416 -0.5031 0.4263 0.5938 -0.0798 0.192 0.0569 -0.0012 0.2259 -0.026 0.1846 -14.1864 1.4011 20.7903 32 1.0954 -0.3183 -0.1377 1.1683 0.1616 1.7124 0.0734 0.3231 -0.1094 -0.2112 -0.1145 -0.0523 0.3408 -0.1653 0.04 0.2861 0.0369 -0.0057 0.2445 -0.0123 0.1693 -14.1522 -7.1348 -5.9117 33 1.2086 0.0298 -0.0132 1.329 0.0544 2.0778 0.1151 0.2423 -0.1293 -0.3617 -0.235 0.0927 -0.6203 -0.016 -0.0623 0.2214 0.0302 -0.0095 0.189 0.0299 0.1759 -16.6554 5.028 -0.9004
Refinement TLS group Show large table (6 x 33) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 2 through 25 )A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 26 through 75 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 76 through 115 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 116 through 138 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 139 through 207 )A0 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 208 through 224 )A0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 2 through 18 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 19 through 38 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 39 through 48 )B0 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 49 through 75 )B0 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 76 through 97 )B0 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 98 through 109 )B0 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 110 through 146 )B