Software Name Version Classification PHENIX(1.20.1_4487: ???)refinement XDSdata reduction XDSdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.84→39.47 Å / SU ML : 0.17 / Cross valid method : THROUGHOUT / σ(F) : 1.36 / Phase error : 16.96 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.182 10299 5 % Rwork 0.1525 - - obs 0.154 205966 99.95 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 1.84→39.47 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 15355 0 16 1576 16947
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.018 15713 X-RAY DIFFRACTION f_angle_d1.479 21272 X-RAY DIFFRACTION f_dihedral_angle_d14.342 5792 X-RAY DIFFRACTION f_chiral_restr0.108 2287 X-RAY DIFFRACTION f_plane_restr0.019 2808
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 (%)1.84-1.87 0.269 337 0.2237 6412 X-RAY DIFFRACTION 99 1.87-1.89 0.2594 340 0.2056 6457 X-RAY DIFFRACTION 100 1.89-1.91 0.2313 338 0.1873 6430 X-RAY DIFFRACTION 100 1.91-1.93 0.2287 340 0.1751 6462 X-RAY DIFFRACTION 100 1.93-1.96 0.2047 342 0.1598 6486 X-RAY DIFFRACTION 100 1.96-1.99 0.2005 340 0.1592 6456 X-RAY DIFFRACTION 100 1.99-2.02 0.1934 342 0.1586 6500 X-RAY DIFFRACTION 100 2.02-2.05 0.1929 338 0.1594 6427 X-RAY DIFFRACTION 100 2.05-2.08 0.1969 341 0.1533 6472 X-RAY DIFFRACTION 100 2.08-2.11 0.2158 343 0.1573 6514 X-RAY DIFFRACTION 100 2.11-2.15 0.1938 340 0.1611 6475 X-RAY DIFFRACTION 100 2.15-2.19 0.1944 340 0.1508 6454 X-RAY DIFFRACTION 100 2.19-2.23 0.1927 341 0.1547 6484 X-RAY DIFFRACTION 100 2.23-2.27 0.1913 344 0.1547 6532 X-RAY DIFFRACTION 100 2.27-2.32 0.1864 340 0.1573 6462 X-RAY DIFFRACTION 100 2.32-2.38 0.1895 342 0.1557 6500 X-RAY DIFFRACTION 100 2.38-2.44 0.1814 343 0.1598 6513 X-RAY DIFFRACTION 100 2.44-2.5 0.2013 342 0.1527 6493 X-RAY DIFFRACTION 100 2.5-2.58 0.1965 343 0.1563 6525 X-RAY DIFFRACTION 100 2.58-2.66 0.1785 344 0.1557 6534 X-RAY DIFFRACTION 100 2.66-2.76 0.1955 342 0.154 6498 X-RAY DIFFRACTION 100 2.76-2.87 0.1878 343 0.1577 6507 X-RAY DIFFRACTION 100 2.87-3 0.1785 346 0.1551 6572 X-RAY DIFFRACTION 100 3-3.15 0.1898 344 0.155 6545 X-RAY DIFFRACTION 100 3.15-3.35 0.1855 346 0.1562 6576 X-RAY DIFFRACTION 100 3.35-3.61 0.1534 345 0.142 6556 X-RAY DIFFRACTION 100 3.61-3.97 0.1582 347 0.1325 6589 X-RAY DIFFRACTION 100 3.97-4.55 0.1331 349 0.1221 6636 X-RAY DIFFRACTION 100 4.55-5.73 0.1735 352 0.1425 6684 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 38) 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 1.9518 1.5261 1.0659 8.6777 4.5579 6.7541 0.1221 -0.3499 0.0613 0.7532 -0.2237 0.484 0.1096 0.0081 0.1109 0.2203 -0.0171 0.039 0.1792 0.018 0.1292 -0.2385 -25.8551 -26.5217 2 5.7639 1.6636 0.4927 2.6215 3.2016 4.4362 0.0042 -0.3351 -0.0381 0.321 -0.0271 -0.1858 0.2381 -0.0537 0.022 0.1491 0.0206 -0.0358 0.0983 0.0063 0.1164 7.1522 -29.4137 -33.2894 3 0.7062 -0.3217 0.3743 1.938 -0.6014 1.3223 0.0249 -0.1237 -0.0027 0.242 0.0237 -0.0237 0.0338 0.0108 -0.0474 0.1192 -0.005 -0.0075 0.1148 -0.0221 0.094 5.8785 -10.6903 -34.3339 4 1.4474 0.5998 -0.7014 2.835 -1.9363 6.7655 0.048 -0.1592 0.0706 0.2136 0.0187 0.1476 -0.2155 -0.1028 -0.0503 0.1027 -0.0068 0.0031 0.0918 -0.0388 0.1171 2.9019 1.1384 -34.937 5 4.1966 -2.1205 -4.8373 4.5757 5.002 8.7135 -0.005 -0.0735 0.1453 0.1746 0.0246 0.0939 0.084 0.039 -0.0113 0.1195 0.0032 -0.0174 0.0636 0.0231 0.0994 11.0623 7.1359 -31.1582 6 1.8955 -0.6782 -0.1 2.1333 0.2531 2.224 0.0142 -0.0584 0.1049 0.0734 0.0592 -0.1913 -0.0984 0.1744 -0.0668 0.1027 -0.0145 -0.0004 0.0938 -0.0181 0.1167 20.7959 9.9345 -42.4988 7 1.0703 -0.4315 -0.2544 2.7703 1.8899 3.1668 0.0479 -0.0532 -0.0394 0.1388 0.0715 -0.1873 0.0581 0.1961 -0.1262 0.1023 0.0098 -0.0166 0.1052 0.0115 0.1295 21.0203 -4.1962 -39.2009 8 3.2448 0.8346 2.8418 3.8575 3.1414 9.4247 0.0332 -0.3128 0.0407 0.5333 -0.0673 -0.1146 0.2553 -0.034 0.0306 0.1567 0.0154 -0.033 0.0985 0.0008 0.1421 18.3829 -12.1376 -29.2724 9 3.6158 1.4725 -0.2903 4.945 -1.319 3.0383 0.073 -0.2848 0.0448 0.3921 -0.077 0.2687 0.0215 -0.1483 0.0067 0.1261 0.0128 0.0166 0.1382 -0.018 0.0985 -12.712 -8.8163 -39.7292 10 1.0237 -0.4989 -0.0195 1.7952 -0.0252 0.5397 -0.0192 -0.1191 -0.05 0.2395 0.0333 0.098 0.0408 -0.0591 -0.0176 0.1216 -0.0113 0.0026 0.1216 0.0048 0.0785 -9.6006 -28.8944 -43.1134 11 4.8654 3.4332 -5.4096 4.5508 -2.136 7.4951 0.0707 -0.0592 0.0353 0.33 0.0636 0.0734 0.0605 -0.1607 -0.1149 0.1251 0.0222 0.0044 0.0867 0.0242 0.1236 -15.5262 -43.644 -46.7311 12 1.8802 -0.2509 0.103 1.4112 -0.2545 1.4558 -0.0405 0.0449 -0.0744 -0.0154 0.0434 0.0426 0.1011 -0.0493 -0.0041 0.104 -0.0065 0.0082 0.0748 -0.0045 0.0833 -9.905 -46.7026 -60.4401 13 5.6752 2.4172 -2.778 2.2717 -1.7628 3.1414 -0.0943 0.2227 -0.0451 -0.0873 0.0796 0.1 0.0505 -0.1138 0.0102 0.1145 0.0304 0.004 0.0607 -0.0183 0.1001 -13.8997 -35.4527 -60.7725 14 4.0244 2.4821 -2.2381 4.2648 -2.137 2.3668 0.0476 -0.0528 -0.0094 -0.0135 -0.048 0.0335 0.017 -0.0729 -0.0166 0.1166 0.0354 0.0041 0.0684 -0.0562 0.04 -11.216 -28.4466 -57.2535 15 5.6804 3.4 -3.7715 4.9434 -0.9367 3.4689 0.1081 0.0624 0.2298 0.1377 -0.0405 0.4066 0.0129 -0.2447 -0.0532 0.1227 0.0121 -0.0236 0.1261 0.0146 0.1016 -20.3123 -24.3915 -52.5513 16 4.9052 1.2726 -5.3693 1.2909 -0.4523 7.2112 0.038 -0.0595 0.2 0.0652 -0.1557 -0.6981 0.0596 0.6369 0.089 0.1707 0.0725 0.0243 0.2551 0.0662 0.3991 11.4188 -49.7576 -67.4644 17 3.5094 -0.6794 -0.281 7.2785 0.3235 3.8118 -0.0815 -0.0635 0.0548 -0.3497 -0.2307 -0.7498 -0.1373 0.2107 0.2535 0.1233 0.0028 0.0445 0.2558 0.0286 0.2308 16.0467 -35.9485 -78.6308 18 1.3391 0.4757 -0.8078 1.5901 -0.4619 1.4377 -0.1076 0.2293 -0.0037 -0.3837 0.1009 -0.1882 -0.0135 0.0412 -0.0034 0.2159 -0.0511 0.0441 0.2077 -0.0261 0.1362 6.6862 -31.2179 -89.3227 19 3.7723 3.7488 3.6102 6.939 6.3291 9.8468 -0.1633 0.0193 0.0863 -0.1854 0.3153 -0.3145 -0.3456 0.3257 -0.1675 0.0877 0.0309 0.0123 0.1369 0.024 0.1747 9.285 -30.1593 -78.6079 20 0.6844 2.03 -1.118 6.9324 -2.6117 3.9215 -0.1797 0.1144 -0.1161 -0.4977 0.0786 -0.2578 0.2319 -0.0151 0.1171 0.0214 0.033 0.0229 0.1665 -0.0036 0.1362 -0.1169 -48.3284 -74.3946 21 0.9278 0.1833 -0.3049 1.1067 0.3129 3.7679 -0.0676 0.2099 0.085 -0.2791 0.0142 -0.1503 -0.2452 0.2583 0.0487 0.1795 -0.0048 0.0133 0.1889 0.0511 0.1807 3.0642 1.335 -75.6369 22 5.8982 -2.9809 7.2482 3.278 -5.4116 2.018 -0.1959 -0.0458 0.4904 -0.0031 0.1867 -0.0588 -0.845 -0.1591 0.0538 0.25 -0.0023 -0.0266 0.132 0.0335 0.2477 -3.9278 14.3279 -67.2518 23 0.5559 0.1445 -0.0642 1.243 0.1233 1.0567 -0.0382 0.0795 0.1801 -0.1528 -0.0011 0.286 -0.1734 -0.2115 0.0285 0.1349 0.0423 -0.041 0.1663 0.0228 0.1957 -17.5226 -0.3795 -66.471 24 1.8066 -0.2946 0.946 2.7092 -1.2717 4.1503 -0.0277 0.282 0.0163 -0.3515 -0.0035 0.0035 0.0092 0.062 0.0414 0.1277 0.0062 0.0148 0.1391 0.0034 0.1159 -6.9751 -9.0217 -75.5843 25 4.932 -1.3025 -5.2987 2.5098 2.4969 7.0332 0.3697 0.7044 -0.0122 -0.5245 -0.3134 0.2475 -0.0376 -0.4211 -0.047 0.3022 0.1007 -0.043 0.2707 0.0575 0.2221 17.4279 12.7162 -64.8636 26 5.4778 2.2169 -0.5191 8.5783 0.0699 4.6319 0.192 0.2115 -0.287 -0.737 -0.2119 -0.0108 -0.0047 -0.2161 0.0065 0.2169 0.0962 0.0182 0.3187 -0.0124 0.1415 27.8003 -1.2539 -76.7538 27 1.1019 -0.137 1.1445 6.9232 5.5853 6.7702 0.1126 -0.0066 0.0881 -0.2633 -0.2772 0.2858 -0.2673 -0.4228 0.1691 0.1625 0.069 0.0416 0.2163 0.0133 0.1586 24.254 6.181 -61.6545 28 5.4692 0.9371 0.5945 6.1956 1.9618 3.8153 0.0323 0.6642 -0.3185 -0.7941 -0.0187 0.1908 -0.2164 -0.276 -0.0142 0.3273 0.0901 -0.0066 0.3096 0.0011 0.1748 29.5741 -0.2972 -84.559 29 2.0504 -1.7997 -0.3871 4.3616 -0.7834 3.7387 0.1696 0.1991 0.0567 -0.3072 -0.1817 -0.0465 -0.1359 -0.0201 0.0204 0.1383 0.0093 0.0293 0.2056 -0.0378 0.154 40.1724 -5.3015 -76.455 30 1.1812 -0.092 -0.3173 1.9634 0.1785 3.2535 0.0152 0.0772 -0.0879 -0.0929 0.0092 -0.345 0.1334 0.3331 -0.0289 0.1176 0.0271 0.0235 0.2101 -0.0427 0.2466 45.3004 -11.3617 -68.6928 31 0.913 -1.139 -0.5766 4.0206 1.2912 1.2397 0.017 0.0655 0.0022 -0.151 0.0302 -0.1951 -0.0347 0.0647 -0.0407 0.1148 0.0077 0.0046 0.1782 -0.0138 0.1207 31.1412 -0.0509 -59.7876 32 6.3587 -2.568 -0.3695 6.6328 -2.5971 7.4469 0.2716 0.5565 -0.3171 -0.8327 -0.2795 -0.3357 0.5413 0.1311 -0.0033 0.2322 0.048 0.0425 0.2599 -0.1029 0.3069 30.4549 -45.4815 -64.769 33 8.1917 -1.0721 -7.3642 0.8908 1.8604 7.6752 -0.0339 0.3526 -0.286 -0.1228 -0.0042 -0.0431 -0.0047 -0.2571 0.0164 0.1598 0.0339 -0.051 0.1235 -0.0416 0.1964 21.6662 -35.9995 -56.2841 34 4.0824 4.6471 -1.2812 5.3135 -1.576 0.6466 -0.151 0.1064 -0.2943 -0.3072 0.0896 -0.4584 0.0933 0.1069 0.0652 0.182 0.0629 0.0223 0.2286 -0.0283 0.2634 32.6302 -36.3463 -61.0155 35 2.0208 -6.4282 -2.6437 4.5258 0.9877 2.9199 -0.4507 -0.2066 -0.8257 0.1213 0.1797 -0.0328 0.5703 0.1641 0.2154 0.2289 0.0433 -0.0445 0.1676 -0.0438 0.3896 23.297 -51.316 -49.8349 36 1.0985 0.0078 -0.3705 1.0298 0.1384 0.5912 0.0239 -0.1862 -0.1984 0.2553 0.0032 -0.3966 0.1535 0.2086 -0.016 0.216 0.068 -0.1002 0.2166 0.0163 0.2892 29.1637 -36.3864 -37.6673 37 2.124 -2.0787 -0.3726 4.79 -0.5599 1.9412 -0.0317 -0.1141 0.4186 0.006 0.0592 -0.7675 0.0062 0.2507 -0.0267 0.1422 0.0129 -0.0258 0.1595 -0.0408 0.2124 32.2715 -23.864 -47.159 38 7.0492 -3.6229 -0.405 3.8525 -0.0831 1.4805 0.1247 0.2614 -0.0332 -0.1617 -0.1152 -0.3962 0.002 0.1733 -0.012 0.1355 0.0168 -0.013 0.1392 -0.0474 0.182 29.8015 -30.3788 -53.9625
Refinement TLS group Show large table (4 x 38) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 8 through 27 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 28 through 46 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 47 through 129 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 130 through 159 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 160 through 182 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 183 through 252 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 253 through 329 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 330 through 357 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 8 through 46 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 47 through 159 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 160 through 182 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 183 through 252 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 253 through 297 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 298 through 329 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 330 through 357 )16 X-RAY DIFFRACTION 16 chain 'C'