Software Name Version Classification HKL-2000data scaling PHENIX1.9_1692refinement PDB_EXTRACT3.15 data extraction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.3→48.667 Å / SU ML : 0.3 / Cross valid method : FREE R-VALUE / σ(F) : 1.36 / Phase error : 25.16 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2378 2724 4.77 % Rwork 0.2001 54362 - obs 0.2019 57086 99.34 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 150.55 Å2 / Biso mean : 59.8255 Å2 / Biso min : 26.73 Å2 Refinement step Cycle : final / Resolution : 2.3→48.667 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 7103 0 0 345 7448 Biso mean - - - 53.24 - Num. residues - - - - 911
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.009 7263 X-RAY DIFFRACTION f_angle_d1.454 9811 X-RAY DIFFRACTION f_chiral_restr0.061 1111 X-RAY DIFFRACTION f_plane_restr0.007 1245 X-RAY DIFFRACTION f_dihedral_angle_d15.732 2693
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 2 B4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 3 C4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 4 D4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 5 E4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 6 F4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 7 G4348 X-RAY DIFFRACTION 17.414 TORSIONAL1 8 H4348 X-RAY DIFFRACTION 17.414 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 19
Show large table (7 x 19) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.2818-2.3233 0.3244 126 0.262 2476 2602 88 2.3233-2.3679 0.3367 147 0.2679 2817 2964 100 2.3679-2.4163 0.3097 130 0.2467 2856 2986 100 2.4163-2.4688 0.2907 143 0.2468 2859 3002 100 2.4688-2.5262 0.2803 148 0.2383 2835 2983 100 2.5262-2.5894 0.2846 134 0.2425 2842 2976 100 2.5894-2.6594 0.292 145 0.2446 2860 3005 100 2.6594-2.7377 0.3026 145 0.24 2849 2994 100 2.7377-2.826 0.292 149 0.2377 2875 3024 100 2.826-2.927 0.3203 132 0.2464 2849 2981 100 2.927-3.0442 0.2662 156 0.2439 2879 3035 100 3.0442-3.1827 0.2834 130 0.2428 2861 2991 100 3.1827-3.3505 0.2595 127 0.23 2907 3034 100 3.3505-3.5603 0.217 127 0.215 2892 3019 100 3.5603-3.8351 0.2572 134 0.2013 2903 3037 100 3.8351-4.2209 0.2104 130 0.172 2917 3047 100 4.2209-4.8312 0.1694 173 0.1394 2895 3068 100 4.8312-6.0849 0.1893 178 0.1441 2934 3112 100 6.0849-48.6781 0.2267 170 0.1894 3056 3226 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 52) 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 4.2636 -0.5513 -0.7994 3.6253 1.1334 1.9954 -0.0808 -0.6163 0.5021 0.1781 0.0317 -0.2488 0.1111 0.0628 -0.0104 0.2654 0.0337 -0.0722 0.3722 -0.0258 0.3882 -9.6613 -22.9392 10.6199 2 6.1378 0.1016 2.1639 3.2964 1.0421 3.0848 0.01 -0.6038 -0.3997 0.1076 0.1087 0.309 0.1333 0.0164 -0.0374 0.2976 -0.0435 -0.0228 0.4625 0.0667 0.4045 -20.3697 -29.3492 13.2314 3 4.0871 -2.9204 0.3122 5.1376 -0.5322 3.1347 -0.2334 -0.5308 0.1484 0.4778 0.1736 -0.7553 -0.0097 0.1026 0.0483 0.349 -0.0412 -0.0855 0.5503 0.0403 0.3989 -9.9378 -28.6627 17.6553 4 7.5128 -5.0337 0.3848 5.5499 -0.5161 0.8231 -0.1744 0.1621 -0.2068 0.1193 0.2208 0.1174 -0.0804 -0.002 -0.0179 0.2656 -0.0125 0.0385 0.3946 0.0049 0.4338 -20.6283 -23.2302 4.3406 5 2.224 -2.665 1.4265 7.0152 -2.1125 7.4585 -0.3337 0.2882 -0.9123 0.9261 0.1269 0.3911 0.2142 0.833 -0.0217 0.362 -0.0099 0.0285 0.4514 0.0676 0.3876 -3.7862 -30.4566 7.7163 6 4.593 0.9417 -1.6377 1.8397 -0.8414 5.8953 -0.0574 0.1458 -0.0404 -0.4399 -0.0737 -0.2468 0.0615 0.4624 0.1779 0.3772 0.0289 0.0103 0.3498 0.0501 0.3526 -17.1046 -7.1311 -21.0368 7 4.7992 -0.8855 0.081 3.9274 -0.1945 4.1298 0.2343 -0.0112 -1.1817 -0.5141 -0.5301 0.1655 0.8486 0.3913 0.2999 0.6371 0.0617 0.0134 0.3598 0.0264 0.4238 -19.8782 -16.6529 -27.2684 8 7.6355 -3.7047 -0.6565 2.6189 0.4994 0.1013 -0.3551 0.2421 -0.1463 -0.1894 0.1049 0.5141 0.7979 -0.0936 0.3803 1.1496 -0.0654 0.0464 0.4994 0.1089 0.4427 -22.0805 -12.018 -34.7589 9 6.5159 -1.95 -0.5947 7.1331 -1.0644 6.1204 0.08 -0.2791 0.1879 -0.789 -0.0897 -0.2078 0.0264 0.2159 -0.1652 0.4464 -0.0381 0.0415 0.3774 0.0361 0.3134 -19.5867 -3.7046 -28.5183 10 8.0942 0.2573 3.1536 3.1018 -2.7083 3.8339 0.9308 0.3071 -0.9286 -0.8218 -0.5313 0.5748 0.7473 0.406 -0.538 0.5089 0.0277 -0.0552 0.4062 -0.0576 0.3971 -17.1176 -18.5417 -18.5656 11 8.2658 -3.1385 0.7858 9.2683 0.8918 5.6235 -0.1476 -0.5563 0.2632 -0.0422 0.6414 1.0332 -0.5744 -0.6076 -0.3555 0.4092 0.0874 0.0904 0.4007 0.112 0.3031 -24.7621 -2.4939 -17.8501 12 1.9462 -0.6773 -0.7386 1.7365 1.1235 3.1881 -0.1921 0.1553 -0.0015 -0.1119 0.0964 -0.3301 0.2238 0.0904 0.2163 0.5809 -0.0378 0.0213 0.2686 0.0544 0.4739 0.6647 15.4694 -13.2617 13 4.8531 0.5626 0.2133 4.7463 1.5125 6.2945 -0.2763 0.3753 0.3634 -0.6073 -0.201 0.1915 -0.153 -0.3295 0.329 0.545 -0.059 -0.0151 0.3671 0.072 0.4405 -5.7348 20.2446 -22.4951 14 9.1302 5.1523 1.1111 6.7551 3.2281 3.103 -0.4809 1.1363 1.0356 -0.2983 -0.0749 -0.0876 -0.8767 0.5561 0.8677 0.9724 -0.3066 0.0606 0.5727 0.1544 0.5458 2.3318 24.5004 -29.652 15 3.8585 2.3852 0.2372 3.6054 -0.1499 2.2526 -0.2878 0.2906 0.5017 -0.0941 0.1352 0.0696 -0.3378 0.198 0.1352 0.5887 -0.0542 0.0345 0.2702 0.0334 0.4448 -0.8781 18.7974 -18.0002 16 5.2255 0.1831 0.1866 4.5861 -1.1226 3.4525 -0.4571 -0.5529 0.8019 0.2263 0.2437 -0.7183 -0.609 0.1645 0.3006 0.5323 -0.0444 -0.0039 0.3003 -0.0917 0.6063 1.6165 23.3432 -6.9708 17 3.1415 -0.9817 -1.2654 3.2153 1.1914 3.522 -0.0978 -0.0788 0.3855 -0.1387 -0.0514 -0.2597 -0.543 -0.0495 0.0858 0.3418 0.0412 -0.0756 0.4091 -0.0246 0.5619 17.9417 -4.5161 5.5361 18 9.6732 -7.357 0.817 5.8455 -1.7536 4.3649 -0.4801 -0.1766 -0.3805 0.6036 0.1135 0.0066 -0.0499 -0.0102 0.4505 0.3361 -0.0248 -0.0117 0.393 0.0121 0.4341 27.7551 -12.0008 -3.0492 19 6.1836 -1.3876 1.1833 5.9566 -1.444 5.5024 0.036 0.6428 0.9631 -0.5429 -0.0893 -0.2067 -0.8454 -0.6234 0.1438 0.5821 0.0858 -0.0291 0.4925 0.0748 0.5165 18.6742 5.0887 -10.0433 20 1.532 0.1295 -0.765 2.8156 -4.4045 7.1003 0.474 -0.3874 1.0933 0.7359 -0.1798 -0.93 -1.4721 1.134 -0.3208 0.7004 -0.1073 0.0839 0.4698 -0.0262 0.9174 27.6466 9.8807 -1.0864 21 2.3799 -0.8445 -1.5954 4.997 -1.6981 5.107 0.3072 0.609 0.311 -0.8437 -0.246 -0.5732 -0.3597 0.432 -0.0326 0.5903 -0.0072 0.1143 0.5018 -0.0465 0.5343 26.7386 1.0382 -12.883 22 9.7065 -1.9372 0.3895 7.6346 1.8754 7.2664 0.1859 -0.6843 1.179 0.5443 -0.1695 -0.625 0.8487 -0.0176 -0.2076 0.3701 -0.0703 -0.0232 0.3827 -0.103 0.6273 31.8451 -7.8167 -0.3148 23 7.658 -5.5958 2.9408 4.144 -2.7535 2.9112 -0.003 0.1657 1.6105 -0.2002 -0.4997 -1.4337 -0.2801 -0.0976 0.332 0.573 0.0015 -0.0201 0.4243 0.0252 0.7481 18.6205 10.4356 -3.0254 24 6.1445 -3.6881 0.1368 8.7688 -2.2846 6.1429 -0.5588 -1.2249 0.1343 0.5138 0.9057 -0.7415 0.3991 0.1114 -0.4224 0.3519 0.0572 -0.0864 0.4695 -0.0605 0.3523 23.2589 -6.2534 4.3009 25 0.9772 -0.5941 -1.9285 3.481 0.2695 3.8307 0.0733 0.319 0.0685 -0.3019 0.0164 0.3685 -0.0582 -0.1822 -0.0816 0.249 0.0066 -0.1025 0.4015 0.0177 0.428 -4.4899 -29.2259 -8.7823 26 6.0224 0.4149 1.2482 2.8569 -1.3136 2.8976 0.0028 0.6475 0.0875 -0.183 0.0225 -0.2031 0.0309 0.1074 0.0058 0.2841 0.0588 -0.0013 0.467 -0.014 0.3259 11.1889 -27.4759 -14.02 27 5.5356 2.5154 -0.6483 4.8803 -0.9902 3.1743 -0.2875 0.4925 0.0347 -0.337 0.3305 0.1287 0.1534 -0.1808 -0.0871 0.2808 0.0433 -0.0174 0.4206 -0.0047 0.3157 1.4018 -30.6283 -15.9183 28 6.1218 4.1745 0.6117 6.0317 0.2631 1.1455 -0.0198 -0.024 -0.1002 -0.0727 0.1423 -0.3744 -0.2522 -0.2791 -0.1356 0.2228 0.0436 0.0274 0.3659 0.0308 0.411 13.1468 -23.6326 -4.6549 29 2.5071 -0.4248 -1.5387 5.8163 0.7366 4.5114 0.0746 -0.3126 -0.035 0.293 -0.1403 0.4018 0.5467 -0.2403 -0.0176 0.2258 0.0442 -0.0153 0.269 0.0116 0.2894 -3.9128 -31.0624 -7.1074 30 4.9291 4.5584 -1.9802 4.1709 -2.0547 3.9257 0.0961 0.2174 0.2691 0.2935 0.0458 0.0719 -0.3468 -0.2111 -0.1439 0.3128 -0.007 0.0882 0.3188 -0.0247 0.3922 -25.4372 -5.4448 -7.9702 31 7.8492 5.4049 0.5935 4.4692 -0.0974 4.3202 -0.1295 0.1914 -0.2904 0.7465 0.2667 0.1823 -0.023 -0.5984 0.1969 0.3122 -0.0015 0.0078 0.4234 -0.0106 0.3899 -35.3816 -11.9511 1.1129 32 3.8038 0.6016 -0.197 3.8237 -0.816 4.0931 0.1503 -0.1278 0.4777 0.2942 -0.1497 -0.1839 -0.7842 0.0353 0.0581 0.4583 0.0054 -0.0056 0.3284 -0.0065 0.3569 -26.8483 5.9109 6.5482 33 9.1077 -5.3559 -5.4083 3.3141 3.0032 3.698 0.5959 0.4658 1.9876 -1.0074 0.3196 -0.6647 -0.1086 -1.3195 -0.6844 0.8611 0.1115 -0.1085 0.5072 0.0118 0.6336 -35.0783 10.3744 -4.0516 34 9.6295 3.8189 2.5333 7.6049 5.871 4.5933 -0.5401 -0.2391 1.2478 0.0177 -0.8788 0.872 -0.389 0.2218 1.2487 0.4201 0.0918 0.0686 0.4819 0.004 0.4088 -35.2342 6.7581 9.0027 35 0.4309 1.7557 0.7112 8.1295 4.9818 4.7442 -0.4549 -0.0842 -0.1492 0.6014 -0.6049 1.1927 0.1403 -1.4672 1.0283 0.5326 0.0595 0.2233 0.8277 -0.0294 0.6568 -41.4984 0.362 6.4174 36 2.4942 3.4686 2.3684 4.8514 3.4974 2.9138 0.0036 -0.2782 -0.757 0.1861 0.2213 -0.7425 -0.1589 0.4239 0.1302 0.5207 0.0029 0.0032 0.3966 0.1122 0.352 -27.8406 -0.5353 11.1983 37 8.0286 1.2967 1.7882 6.2499 -1.5318 7.4565 0.2515 -0.1566 0.0199 -0.2092 0.0215 0.9311 0.0211 -1.1385 -0.141 0.27 0.0287 0.0054 0.5148 0.0712 0.5318 -39.3892 -8.2134 -2.2134 38 4.5016 5.5009 2.5464 8.6541 3.0993 3.713 -0.3497 0.229 0.769 0.3751 0.1172 0.8865 -0.547 0.2279 0.16 0.5185 0.0559 -0.0014 0.3498 -0.012 0.4422 -26.4729 10.4313 -1.0033 39 7.6477 4.7001 0.2222 9.5605 4.4692 6.9372 -0.1583 0.5924 -0.1475 -0.0647 0.2273 0.3205 0.5245 -0.0931 -0.1231 0.4133 0.0358 -0.0302 0.2362 0.0346 0.2776 -30.6283 -7.2503 -6.6288 40 3.3384 -0.106 -0.2435 1.8269 0.9573 5.3059 -0.1127 -0.524 0.7021 -0.0349 -0.1689 -0.106 -1.2038 -0.2356 0.1626 0.532 0.0151 -0.1321 0.4824 -0.1765 0.5669 15.3661 1.6459 15.5715 41 5.3866 2.2871 1.0776 7.7677 1.6041 0.5915 0.5928 -0.2197 0.3105 1.1643 -0.8911 1.424 0.6238 -0.8775 0.1283 0.661 -0.0739 0.0969 1.0064 -0.2424 0.6777 0.2914 -11.223 21.2569 42 4.3076 2.2271 1.2075 2.1766 -0.4831 3.8359 0.1714 -1.0236 -0.434 -0.4094 -0.2807 -0.7353 0.4536 0.0205 0.0863 0.6307 0.1062 -0.1575 0.759 0.0209 0.5182 16.3643 -11.8822 20.7881 43 0.013 -0.317 -0.2048 8.3851 5.0569 3.2174 0.0945 -1.1938 -1.2234 2.0942 -0.84 0.2777 1.3734 -0.1949 0.6896 1.083 -0.2298 -0.0417 1.1872 -0.0526 0.5943 9.4094 -12.892 29.0233 44 0.5039 0.676 -1.3178 3.5995 -0.5834 3.6413 0.0358 -1.6304 -0.1148 1.2392 -0.1802 0.1564 0.0862 -1.2602 0.5404 0.7921 -0.1084 0.0883 1.0295 -0.224 0.6525 8.0356 -4.139 28.7036 45 4.021 1.8123 0.8916 5.0339 2.8817 4.7084 -0.0071 -0.927 0.0972 0.8359 0.0913 -0.6808 -0.5853 0.377 -0.1247 0.5221 -0.0374 -0.1661 0.5538 -0.05 0.5017 17.5756 -2.1968 21.9886 46 5.0832 -1.3475 -3.4227 7.545 0.7762 2.3363 0.6902 -1.1328 -0.693 0.3105 0.1412 -1.2994 -0.2221 1.5784 -0.809 0.4573 -0.1636 -0.0879 0.9525 0.0738 0.643 5.7308 -22.222 16.8214 47 5.6248 0.2173 0.8768 0.7286 0.9166 4.5499 0.3545 -0.6698 0.3871 0.5859 -0.5396 -0.7249 -0.7236 0.376 0.2401 0.4875 -0.0891 -0.1311 0.5529 -0.0688 0.4819 16.9212 -1.5252 14.8992 48 4.4903 -1.0715 -0.4014 3.2896 -0.6709 3.3698 -0.5005 -1.0488 0.0581 0.4952 0.42 0.1494 0.0694 -0.1112 0.1433 0.6359 0.1299 0.0678 0.4767 -0.0236 0.5528 -7.2727 17.9052 10.0206 49 7.3229 0.4079 -1.2958 3.1832 2.076 4.7609 -0.4258 -1.6238 0.5966 0.254 0.5233 -0.7583 -1.4378 1.5679 -0.3191 0.8942 0.2157 -0.2605 0.9727 -0.318 0.9558 2.7661 26.3604 14.2244 50 4.3342 0.2048 -0.955 1.4867 0.5205 3.4736 -0.9174 -1.5864 0.3967 1.3782 0.6796 0.2575 -0.0723 0.0738 0.1149 1.0492 0.3205 0.0755 0.8599 -0.1478 0.6604 -9.2356 22.7185 15.9621 51 2.0082 -4.9717 6.1366 4.6876 -2.4196 3.8812 0.0347 -0.7241 1.3019 -0.0453 -0.5958 -0.9389 -1.3067 -0.9512 0.4531 1.056 0.2076 -0.0907 0.6563 -0.0895 0.5459 9.8417 12.5338 15.5837 52 2.3811 1.7838 -0.6407 4.2889 1.137 2.0499 -0.6696 -0.1175 1.5194 0.1388 0.4371 -0.2054 -0.2061 0.0846 0.223 0.7351 0.0862 -0.0121 0.3621 -0.0834 0.654 -9.5278 24.0345 2.1758
Refinement TLS group Show large table (6 x 52) 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 -1 through 28 ) A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 29 through 59 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 60 through 85 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 86 through 100 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 101 through 112 )A0 6 X-RAY DIFFRACTION 6 chain 'B' and (resid -1 through 34 ) B0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 35 through 54 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 55 through 59 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 60 through 85 )B0 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 86 through 100 )B0 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 101 through 112 )B0 12 X-RAY DIFFRACTION 12 chain 'C' and (resid -1 through 28 ) C0 13 X-RAY DIFFRACTION 13 chain 'C' and (resid 29 through 54 )C0 14 X-RAY DIFFRACTION 14 chain 'C' and (resid 55 through 59 )C0 15 X-RAY DIFFRACTION 15 chain 'C' and (resid 60 through 100 )C0 16 X-RAY DIFFRACTION 16 chain 'C'