Software Name Version Classification PHENIXdev_5533refinement Aimlessdata scaling XDSdata reduction PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.49→46.49 Å / SU ML : 0.16 / Cross valid method : FREE R-VALUE / σ(F) : 1.34 / Phase error : 17.64 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.1678 11681 4.99 % Rwork 0.1466 - - obs 0.1476 234160 99.13 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 1.49→46.49 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 10780 0 66 1286 12132
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 11342 X-RAY DIFFRACTION f_angle_d0.972 15463 X-RAY DIFFRACTION f_dihedral_angle_d13.075 4235 X-RAY DIFFRACTION f_chiral_restr0.079 1796 X-RAY DIFFRACTION f_plane_restr0.008 1995
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.49-1.51 0.2545 386 0.2397 7251 X-RAY DIFFRACTION 97 1.51-1.52 0.2465 355 0.2297 7399 X-RAY DIFFRACTION 99 1.52-1.54 0.2457 381 0.2238 7212 X-RAY DIFFRACTION 98 1.54-1.56 0.2526 386 0.2148 7268 X-RAY DIFFRACTION 98 1.56-1.58 0.2468 421 0.2115 7362 X-RAY DIFFRACTION 99 1.58-1.61 0.2561 385 0.2251 7210 X-RAY DIFFRACTION 97 1.61-1.63 0.2333 418 0.2366 7321 X-RAY DIFFRACTION 99 1.63-1.65 0.2727 406 0.2519 7325 X-RAY DIFFRACTION 98 1.65-1.68 0.2892 366 0.2236 7343 X-RAY DIFFRACTION 99 1.68-1.71 0.2255 370 0.197 7375 X-RAY DIFFRACTION 99 1.71-1.74 0.2183 402 0.1859 7370 X-RAY DIFFRACTION 99 1.74-1.77 0.2 361 0.1759 7442 X-RAY DIFFRACTION 99 1.77-1.8 0.2032 373 0.1676 7292 X-RAY DIFFRACTION 99 1.8-1.84 0.1944 412 0.1593 7402 X-RAY DIFFRACTION 99 1.84-1.88 0.1856 390 0.1481 7374 X-RAY DIFFRACTION 100 1.88-1.92 0.1712 376 0.1466 7399 X-RAY DIFFRACTION 99 1.92-1.97 0.1802 374 0.1547 7445 X-RAY DIFFRACTION 100 1.97-2.02 0.1796 411 0.1612 7372 X-RAY DIFFRACTION 99 2.02-2.08 0.1873 392 0.1591 7418 X-RAY DIFFRACTION 99 2.08-2.15 0.1645 379 0.1392 7468 X-RAY DIFFRACTION 100 2.15-2.23 0.1593 399 0.133 7419 X-RAY DIFFRACTION 100 2.23-2.31 0.1653 411 0.1334 7456 X-RAY DIFFRACTION 100 2.31-2.42 0.1521 400 0.1313 7472 X-RAY DIFFRACTION 100 2.42-2.55 0.1508 355 0.1281 7522 X-RAY DIFFRACTION 100 2.55-2.71 0.1488 394 0.1269 7507 X-RAY DIFFRACTION 100 2.71-2.92 0.1606 404 0.1373 7543 X-RAY DIFFRACTION 100 2.92-3.21 0.1488 373 0.1337 7512 X-RAY DIFFRACTION 100 3.21-3.67 0.1514 428 0.1334 7543 X-RAY DIFFRACTION 100 3.67-4.63 0.128 402 0.1167 7607 X-RAY DIFFRACTION 100 4.63-46.49 0.1612 371 0.15 7850 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 44) 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 4.0586 -0.095 -0.6572 1.1384 0.0575 1.9907 0.0096 -0.2568 0.1157 0.1887 -0.0222 -0.1149 -0.1298 0.2433 0.0141 0.2334 -0.0509 -0.0363 0.1785 -0.0047 0.1364 -21.3699 32.7796 74.1556 2 1.0693 0.1929 0.1306 0.4515 0.1124 1.0431 0.0243 0.0269 -0.0655 0.0864 -0.0332 -0.0578 0.0315 0.0894 0.0064 0.1375 -0.0095 -0.0054 0.1036 0.0185 0.1239 -24.8837 21.9276 57.8628 3 3.1389 1.0483 0.2384 6.1492 -1.0515 2.4806 0.1443 -0.2556 -0.2886 0.4701 -0.1442 -0.3311 0.1395 0.1649 0.0155 0.25 -0.023 -0.0596 0.2599 0.0338 0.1887 -12.9923 19.0308 68.2515 4 6.5246 1.529 -5.2431 2.4675 -1.376 4.2687 -0.1781 -0.6362 -0.8079 0.154 -0.2283 -0.118 0.3922 0.4611 0.3874 0.2594 0.006 0.0114 0.2039 0.0565 0.1976 -39.2159 11.8474 79.6309 5 2.6562 0.2058 -1.6476 0.4765 -0.101 2.1709 0.0187 -0.2522 0.0544 0.1349 -0.0326 0.0088 -0.0986 0.137 -0.016 0.2578 -0.0146 0.0073 0.1802 0.0091 0.151 -42.982 23.8668 84.5876 6 0.7594 0.0386 -0.1603 0.3944 -0.0952 1.2225 0.0335 0.0185 -0.013 0.0611 -0.0169 0.0249 -0.0792 -0.0368 -0.018 0.1651 -0.0009 0.0304 0.1035 0.0093 0.1352 -48.7459 23.9215 67.5363 7 2.9738 -0.5428 -1.5795 5.3053 5.5206 9.3218 0.0335 0.0992 -0.1017 0.3374 -0.3357 0.4816 0.1754 -0.6572 0.2591 0.2177 0.002 0.0624 0.2276 0.0055 0.1943 -63.5966 26.1105 76.0798 8 2.0847 -0.2488 -0.4104 0.29 0.3706 0.9583 0.019 0.1326 0.1027 0.1131 -0.0061 0.0567 -0.1421 -0.0922 -0.0666 0.2113 0.0252 0.0281 0.0994 0.0165 0.1509 -49.6165 35.4541 64.3556 9 0.996 -0.1371 -0.2928 0.1065 0.1388 1.481 0.0483 -0.001 0.1428 0.0786 0.0086 0.0273 -0.2927 -0.0137 -0.0357 0.192 0.0058 0.0317 0.1119 0.0042 0.1418 -50.8461 32.2379 65.1992 10 3.0844 3.3672 -1.3741 9.5861 -2.2106 3.7735 0.198 -0.2689 0.0971 0.2806 -0.1755 -0.0903 -0.2471 0.2063 -0.0069 0.2212 0.0128 0.0339 0.1868 -0.019 0.1434 -53.3663 33.5555 81.7413 11 2.9105 -0.2669 0.3345 0.5807 -0.1486 0.6367 0.0227 0.3834 -0.1152 -0.0866 -0.0471 -0.2107 0.1246 0.5426 0.0232 0.1669 0.0567 0.0096 0.4237 -0.009 0.1852 -12.6746 15.7795 22.8379 12 1.3733 -0.1408 0.014 1.5433 -0.0238 1.2903 0.0587 0.105 -0.0038 0.0849 -0.0472 -0.0922 0.0079 0.2652 -0.0378 0.1159 0.004 0.0004 0.2281 0.0206 0.1074 -18.8359 21.8955 32.1944 13 2.7791 0.7612 -0.9048 1.2332 -0.4195 1.591 0.0346 -0.0065 -0.0277 0.0356 -0.0703 -0.0813 0.0064 0.2397 0.0239 0.116 0.001 -0.0152 0.1596 0.0083 0.0987 -22.4834 22.4771 42.599 14 1.5487 -0.0096 -0.4343 0.4855 0.1188 1.1908 -0.0255 0.0019 0.1101 -0.0359 -0.0104 -0.047 -0.3311 0.0824 0.0294 0.186 -0.0353 -0.0062 0.1797 0.0301 0.1567 -25.6451 33.758 36.2462 15 1.2975 -0.2724 -0.1965 0.4536 0.2462 1.5769 0.0499 0.1334 0.1787 -0.0212 -0.0394 -0.0429 -0.2216 0.1207 -0.0001 0.1691 -0.0256 -0.0066 0.1985 0.0335 0.1668 -23.4338 30.654 37.7092 16 3.9131 -2.986 1.1296 3.8371 -3.1527 4.369 0.2664 0.6132 0.527 -0.2279 -0.4642 -0.4581 -0.2444 0.494 0.263 0.2292 -0.0269 -0.0029 0.4819 0.1171 0.312 -7.9456 30.0604 30.8355 17 0.8615 -0.1532 0.4958 0.7813 0.066 2.4651 0.0323 0.2611 0.0471 -0.1513 -0.0569 -0.0507 -0.111 0.1692 0.0234 0.1629 0.0134 0.0095 0.3032 0.0337 0.1331 -31.6152 26.5532 10.3541 18 0.8727 1.5932 -0.1078 6.5235 -0.729 1.5617 0.0671 0.1034 -0.0254 0.0265 -0.0511 0.233 0.1566 -0.1507 -0.0416 0.1697 0.0092 -0.0003 0.315 -0.0208 0.1713 -42.3963 15.8934 15.6586 19 0.58 -0.3557 -0.5355 1.0777 0.6867 1.6504 0.0196 0.0283 0.0031 0.0346 -0.0214 -0.0193 -0.0102 -0.1056 -0.0006 0.15 0.0009 -0.0113 0.264 0.0046 0.1455 -46.3552 23.7741 27.9531 20 2.9203 0.6949 1.0743 7.0266 1.0941 1.7126 0.0798 0.1596 -0.0627 -0.2288 -0.4222 0.523 -0.2005 -0.6865 0.3814 0.1602 0.0385 -0.0304 0.4165 -0.0581 0.1545 -52.3565 19.4254 7.873 21 1.1514 -0.2458 0.4606 0.4613 0.4055 1.8269 -0.0076 0.0775 -0.1546 -0.051 -0.0286 0.0086 0.1757 -0.1968 -0.0208 0.1561 -0.0269 0.0031 0.2081 -0.0244 0.1327 -42.3999 10.9501 23.4911 22 0.6781 0.1785 0.0824 1.263 0.1249 0.7405 0.0275 0.0611 -0.0365 0.0693 -0.0434 0.0365 0.0493 -0.1244 0.0196 0.1625 -0.0085 -0.0065 0.2701 -0.0177 0.1445 -45.1229 18.3332 24.8195 23 1.2698 -0.6501 -0.7986 2.4289 1.9136 2.3169 0.0089 0.0344 -0.1549 0.0301 -0.0824 -0.0556 0.5714 0.0755 0.0613 0.235 0.0007 -0.0274 0.2943 -0.0224 0.168 -41.1882 7.3722 18.1543 24 2.6274 -3.2783 2.2364 8.788 -5.2231 5.58 0.1625 0.1913 0.011 -0.3008 -0.2056 -0.1738 0.2781 0.0231 0.0233 0.1691 0.0127 -0.009 0.3537 -0.0488 0.1557 -40.8641 12.7325 5.5989 25 1.3397 -0.5153 0.5363 1.7453 0.1883 2.4453 -0.0204 0.4272 0.4265 -0.0852 0.0163 0.2552 -0.4206 -0.4399 0.018 0.2024 0.0995 0.0289 0.5219 0.1199 0.3797 -79.2511 34.3188 44.9207 26 3.0665 0.2732 -1.1154 1.3602 -0.692 3.0732 0.0957 0.1872 -0.0373 0.1073 -0.0425 0.3822 0.0045 -0.5211 0.0735 0.1661 0.0058 0.0449 0.6089 0.0653 0.3543 -87.5739 24.1827 50.6834 27 1.4571 -0.075 -0.0019 0.89 0.0303 0.0052 -0.0212 0.27 0.128 0.0479 0.0367 0.2385 -0.0868 -0.4512 -0.0337 0.1577 0.0592 0.0258 0.4349 0.0453 0.2561 -77.5846 28.9511 48.6824 28 2.653 -0.9974 -0.0109 3.0639 -0.8058 1.7969 -0.0774 -0.0414 -0.2653 0.1745 0.0706 0.206 0.0851 -0.2482 -0.0317 0.1342 -0.0191 0.0302 0.2781 0.0111 0.2105 -70.9283 18.5017 56.8948 29 2.0609 0.1712 -0.0986 0.8636 0.0595 0.8944 -0.0167 0.1264 0.0027 -0.0478 0.0124 0.0844 -0.008 -0.0946 -0.0301 0.1706 0.0225 0.0223 0.1835 0.0105 0.163 -57.8276 25.7359 52.8877 30 9.4279 5.4546 -3.1026 5.6011 -2.1748 4.016 0.1168 -0.5389 -0.0756 0.4939 -0.1184 0.2266 -0.153 -0.1488 -0.0086 0.2074 0.0272 0.073 0.3571 0.0129 0.232 -72.5201 23.5829 68.8356 31 2.4212 0.1027 -0.6616 0.6583 0.0535 1.728 -0.0519 0.0639 -0.2435 0.0446 0.1021 0.1557 0.198 -0.1143 0.1136 0.1751 -0.019 0.0329 0.2092 0.0079 0.2364 -64.9662 12.8081 54.2956 32 1.9895 -0.1164 -0.1223 0.901 -0.1221 1.1943 -0.0238 0.1462 -0.0721 0.0146 0.0591 0.1053 0.0238 -0.1909 -0.0068 0.156 -0.0042 0.0249 0.2141 0.002 0.1618 -61.6152 20.3852 54.4797 33 2.8692 0.5725 -0.0801 1.9562 -0.3522 1.7158 -0.091 0.1558 -0.6967 -0.0355 -0.12 0.2967 0.3382 -0.3073 0.0653 0.2274 -0.0437 0.0629 0.2766 -0.0141 0.3438 -69.7834 9.7185 55.7596 34 2.9656 0.0427 -0.2832 8.5824 2.1478 2.5867 -0.0205 0.1486 -0.4354 0.1447 -0.0828 0.4263 0.266 -0.5141 0.0587 0.211 -0.0331 0.0607 0.4186 0.0038 0.3674 -80.7113 16.2613 60.5399 35 0.6574 -0.0348 0.3706 0.0407 0.1035 0.5943 -0.0161 0.1741 -0.332 -0.0749 0.0551 0.0882 0.2039 -0.268 0.0153 0.2622 -0.2399 0.0012 0.7139 -0.0455 0.3821 -76.4859 6.6654 32.1951 36 0.7817 0.0341 -0.0721 0.2124 -0.0064 0.0059 0.026 0.4067 0.0492 -0.1413 -0.0102 0.1959 -0.0769 -0.4065 0.0322 0.1926 -0.029 -0.0137 0.8666 0.06 0.3146 -79.1042 21.6849 25.7746 37 0.0069 0.0121 -0.0491 0.0339 -0.1409 0.529 -0.0358 0.3231 -0.1038 -0.1065 0.1273 0.168 0.1019 -0.2346 0.0394 0.1711 -0.1736 -0.0553 0.9707 -0.0078 0.3403 -82.0457 14.3398 25.8647 38 1.2874 0.2841 0.3097 0.6502 0.2907 0.6203 -0.0812 0.4865 0.0144 -0.1471 0.113 0.0733 0.0519 -0.4968 0.0317 0.1821 -0.0506 0.0092 0.594 -0.0015 0.2267 -68.2774 20.4493 27.7172 39 1.4416 -0.1023 1.467 1.0609 -0.0277 1.6644 -0.0116 0.2929 0.0402 0.0237 -0.0327 0.1067 0.0052 -0.2199 0.026 0.127 -0.0254 0.0145 0.3245 -0.0075 0.1445 -54.4711 20.0044 31.6957 40 4.2402 -1.532 3.2974 2.2699 -1.2387 3.6842 -0.0138 0.4721 0.1131 -0.2197 -0.0394 0.0878 -0.0415 0.0999 0.0766 0.1964 -0.0573 -0.053 0.8174 0.011 0.1791 -64.1965 21.4853 11.8919 41 0.4674 -0.3748 0.7569 1.0676 -0.4535 1.3027 0.023 0.3852 0.2074 0.0035 0.098 0.158 -0.1514 -0.2597 0.005 0.1271 0.0261 0.0001 0.4267 0.0778 0.2053 -60.8787 32.4533 29.8362 42 1.0867 0.3962 -0.6246 1.3548 -0.5368 1.0305 -0.0329 0.2958 0.0189 -0.0077 0.1076 0.0861 -0.0183 -0.3966 -0.0711 0.1382 0.009 -0.018 0.3618 0.0097 0.1465 -57.5311 25.2328 29.0506 43 2.4786 -0.2889 0.9058 0.5368 -0.8481 1.4232 -0.0792 0.3396 0.4579 -0.1434 0.0014 0.4639 -0.298 -0.4969 0.0902 0.2137 0.0854 0.0197 0.6273 0.0987 0.3218 -66.1313 34.7598 25.2964 44 3.1291 -0.448 0.1258 1.781 0.1732 0.5078 -0.0762 0.0585 0.1849 -0.0159 0.3076 0.1652 -0.0656 -0.4189 0.0747 0.203 0.0215 -0.0252 0.9398 0.0975 0.3056 -74.5693 27.4372 17.3898
Refinement TLS group Show large table (4 x 44) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 55 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 56 through 214 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 215 through 236 )4 X-RAY DIFFRACTION 4 chain 'B' and (resid 1 through 15 )5 X-RAY DIFFRACTION 5 chain 'B' and (resid 16 through 55 )6 X-RAY DIFFRACTION 6 chain 'B' and (resid 56 through 131 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 132 through 144 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 145 through 166 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 167 through 214 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 215 through 236 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 1 through 55 )12 X-RAY DIFFRACTION 12 chain 'C' and (resid 56 through 103 )13 X-RAY DIFFRACTION 13 chain 'C' and (resid 104 through 145 )14 X-RAY DIFFRACTION 14 chain 'C' and (resid 146 through 166 )15 X-RAY DIFFRACTION 15 chain 'C' and (resid 167 through 214 )16 X-RAY DIFFRACTION 16 chain 'C'