Software Name Version Classification PHENIX(phenix.refine: 1.5_2)refinement HKL-2000data reduction SCALEPACKdata scaling PHENIXphasing
Refinement Method to determine structure : SAD / Resolution : 2.5→48.24 Å / SU ML : 0.31 / σ(F) : 0.15 / Phase error : 19.44 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.223 1921 3 % Rwork 0.173 - - obs 0.175 62180 94.5 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 69.19 Å2 / ksol : 0.31 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- -1.3689 Å2 0 Å2 -0 Å2 2- - 4.1167 Å2 -0 Å2 3- - - -2.7478 Å2
Refinement step Cycle : LAST / Resolution : 2.5→48.24 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 9822 0 397 227 10446
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 10416 X-RAY DIFFRACTION f_angle_d1.026 14043 X-RAY DIFFRACTION f_dihedral_angle_d17.593 3715 X-RAY DIFFRACTION f_chiral_restr0.073 1683 X-RAY DIFFRACTION f_plane_restr0.004 1643
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.5-2.5625 0.2262 131 0.1727 4140 X-RAY DIFFRACTION 89 2.5625-2.6318 0.2231 126 0.1552 4186 X-RAY DIFFRACTION 90 2.6318-2.7092 0.2248 135 0.146 4285 X-RAY DIFFRACTION 93 2.7092-2.7967 0.2213 134 0.1441 4302 X-RAY DIFFRACTION 93 2.7967-2.8966 0.1952 141 0.1456 4416 X-RAY DIFFRACTION 95 2.8966-3.0126 0.2153 136 0.1401 4460 X-RAY DIFFRACTION 96 3.0126-3.1497 0.2146 138 0.151 4517 X-RAY DIFFRACTION 97 3.1497-3.3157 0.2246 144 0.1478 4535 X-RAY DIFFRACTION 98 3.3157-3.5234 0.1853 143 0.1599 4588 X-RAY DIFFRACTION 98 3.5234-3.7953 0.2354 111 0.1695 3676 X-RAY DIFFRACTION 78 3.7953-4.177 0.2119 141 0.1619 4682 X-RAY DIFFRACTION 99 4.177-4.781 0.1888 145 0.1548 4708 X-RAY DIFFRACTION 99 4.781-6.0217 0.2186 144 0.1826 4744 X-RAY DIFFRACTION 99 6.0217-48.2477 0.2695 152 0.2272 4942 X-RAY DIFFRACTION 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 50) 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 0.0864 0.0316 -0.1189 0.1852 -0.0473 0.1721 0.314 0.0987 0.0037 -0.4637 0.978 -0.2384 -0.1989 -0.1107 -0.0009 0.8166 -0.0134 0.2332 1.0034 0.2253 0.4169 74.3274 93.3102 85.1424 2 0.0324 -0.068 0.1283 0.1233 -0.2465 0.4489 0.0362 0.0337 -0.0395 0.097 -0.0791 0.1831 -0.1478 -0.1446 -0 0.252 -0.0147 0.0089 0.2633 0.0475 0.2286 56.7769 77.1804 98.3519 3 0.8699 -0.2412 0.7147 0.6704 0.5279 1.4415 0.15 0.4587 0.207 0.2006 0.0142 0.1361 0.0154 -0.3567 -0.0001 0.1675 0.0199 -0.0009 0.2344 -0.0283 0.2466 56.8025 74.8467 107.1288 4 0.0277 -0.0396 -0.0008 0.1132 0.0952 0.1626 1.0033 -0.4187 0.1954 -0.9758 1.1684 -1.115 -0.4352 1.3633 0.0102 0.7099 -0.4635 -0.0395 0.8643 -0.2719 1.1097 71.0317 93.5744 105.3286 5 0.0237 -0.0493 0.0189 0.1228 -0.0583 0.0343 0.1381 0.1397 0.7862 -0.6745 0.9586 0.4453 0.016 0.5173 0.0081 1.4825 -0.7122 0.5987 1.208 -0.4176 1.7928 75.552 100.7641 102.5024 6 0.045 0.0121 -0.1019 0.1457 -0.0848 0.456 -0.0209 -0.0688 -0.0024 -1.0108 -0.2669 0.0621 -1.3215 2.5326 0.0115 0.7237 -0.4137 0.1755 1.0001 0.0385 0.8801 68.7917 97.9499 96.8131 7 1.3249 -0.7491 0.2593 0.5298 -0.1718 1.8088 0.0109 0.1712 0.0568 -0.0472 -0.1141 0.0751 -0.1591 -0.0687 -0 0.1684 -0.0117 -0.0242 0.2492 0.0734 0.1936 50.5352 82.5766 101.4371 8 3.9625 -5.2478 -3.2971 8.5474 4.7275 3.6711 -0.1319 -1.0535 1.1984 -0.4696 1.188 -1.7002 -0.5834 1.3774 0.2234 0.2727 -0.0762 0.083 0.4413 0.0282 0.4299 75.5271 78.5129 110.3209 9 1.7451 -0.8651 0.006 1.1145 -0.4133 1.6153 0.0938 0.3066 0.1422 -0.0047 -0.0126 0.0583 -0.161 -0.1997 -0 0.1699 -0.0122 0.0008 0.217 0.0707 0.1871 48.7709 82.3435 102.2403 10 2.4618 0.1469 2.0029 0.8441 -0.5275 3.1325 1.4527 1.0992 -0.6071 0.3765 -1.426 -1.3136 0.0742 2.1757 0.005 0.6367 -0.2942 -0.1471 0.7106 0.1548 0.6465 73.9577 94.1324 115.7877 11 2.1909 0.4701 0.369 3.7932 -5.2003 7.6146 -0.1659 -0.499 0.2588 0.3712 0.7015 0.0596 -1.2309 0.2115 0.1908 0.4961 -0.4421 -0.3465 1.0028 -0.0225 1.0922 81.6385 97.417 128.5593 12 0.8167 -0.991 -0.0144 1.2351 0.2382 1.0129 0.0564 -0.3927 0.1122 -0.0593 -0.2459 -0.1632 -0.0771 -0.0119 0 0.183 -0.0241 -0.0246 0.1328 0.0132 0.1893 61.1273 82.1531 124.3157 13 1.1758 -1.1765 -0.6126 3.2651 -0.4173 2.4143 0.0877 -0.0694 0.4227 0.1476 -0.007 0.4789 -0.0474 0.0107 0.0041 0.1374 0.002 -0.0064 0.1093 0.0084 0.0857 59.7496 72.4266 124.3377 14 0.0881 -0.1548 0.0093 0.3204 -0.2058 0.7388 0.4678 -1.3184 -0.4469 1.0391 -0.1572 0.2727 1.3299 0.7133 -0.0323 0.6842 0.1951 -0.1729 0.7593 0.199 1.0368 74.2712 80.5489 134.2738 15 0.419 0.0821 0.0343 0.1725 0.0837 0.0394 0.6575 0.1507 -0.6239 -1.7675 0.5787 -1.4655 -0.5942 -0.6801 -0.0205 1.2594 -0.1498 -0.4143 1.5007 -0.491 1.5109 85.5673 86.6378 139.8587 16 0.3084 0.2229 0.0691 0.2199 0.1127 0.0837 -1.0951 -0.429 0.3725 0.5476 -0.9424 -0.3931 -0.5291 0.4683 0.0141 0.9901 -0.0905 -0.1994 1.26 -0.0646 0.456 76.6802 88.7368 138.5214 17 1.2006 -0.7144 -0.7203 0.6419 -0.1051 1.5441 -0.0892 -0.1149 0.1293 0.1924 0.103 0.0557 -0.2919 -0.0482 0.0004 0.2125 0.0011 -0.0469 0.0788 -0.0543 0.2019 56.6025 81.4912 131.8091 18 0.2937 -0.1929 -0.456 0.9807 -0.0584 1.2963 -0.115 -0.253 -0.7817 -0.0083 -0.2784 -1.4838 -0.1096 1.5911 -0.0901 0.1937 -0.0581 -0.0522 0.4851 0.0496 0.505 79.795 69.0824 124.8353 19 0.7847 -0.2527 -0.4678 0.4022 0.3658 1.4065 -0.0428 -0.0837 0.1117 0.1433 -0.0619 0.1445 -0.137 -0.1087 -0.0205 0.1679 -0.0302 -0.0156 0.0919 -0.054 0.1734 55.0904 80.5827 132.4257 20 0.9117 -0.5591 -0.2792 0.5 0.47 0.6697 0.5125 -0.1248 1.5715 -0.3265 -0.5294 -1.2653 -1.6938 0.3734 0.0346 0.4601 0.0069 -0.0959 0.8588 0.1886 0.5693 83.6679 69.3706 141.14 21 1.2751 0.123 -0.2544 0.0785 -0.0923 0.1195 0.3546 -0.4425 -0.2569 -0.135 0.8221 0.2382 0.1176 0.5875 0.0034 1.0211 0.0955 0.2136 1.4289 -0.2637 1.9004 94.5082 58.4225 147.4215 22 0.692 -0.2759 -0.7918 0.6206 0.6628 2.3973 -0.0003 -0.3709 -0.2794 0.192 0.0271 0.0487 0.1065 0.0869 0.021 0.1091 0.035 0.0125 0.0467 0.0892 0.1013 66.5244 57.5133 132.7958 23 5.4429 -4.0636 -0.3735 3.0572 0.4929 2.0332 0.3314 0.1339 -1.3304 -1.8856 -0.3145 0.1636 1.0387 0.2277 0.0714 1.1342 0.2074 0.4012 1.4307 -0.1186 0.4066 78.8861 48.0648 134.3767 24 0.1358 0.1887 0.0325 0.5221 -0.1036 0.1056 -0.7868 0.1068 -0.5909 0.023 -0.5569 0.0099 0.7073 0.0317 0.0106 0.7132 0.176 -0.3831 2.0747 0.301 1.4724 90.0435 42.6067 134.6276 25 0.0689 0.0219 -0.027 0.008 -0.0086 0.0094 0.1181 0.336 0.0476 0.5197 -0.372 0.5345 -0.7518 -0.7709 0.0082 1.0376 0.0445 -1.0399 1.6506 0.4461 2.6402 91.3043 42.7859 142.7624 26 0.2761 -0.0694 0.0657 0.0185 -0.018 0.0206 0.0623 -0.9173 -0.8851 -1.0566 0.2955 -0.0913 0.3947 0.7384 0.0013 0.71 0.005 -0.1225 0.7554 0.3822 0.9803 83.9177 46.0362 143.1434 27 1.5389 1.1673 -0.5801 0.8545 -0.4335 2.038 -0.0443 -0.1545 -0.196 0.2341 -0.0668 -0.0299 0.1655 0.0896 -0.0003 0.267 0.0451 -0.0031 0.1771 0.0482 0.171 62.5563 52.092 139.4345 28 0.0669 -0.01 0.121 0.3463 0.0008 0.2568 -0.2216 0.2015 -0.3516 -0.3284 -0.1074 -1.0323 0.4189 0.6851 -0.003 0.2382 0.0642 0.0223 0.3612 0.0233 0.379 77.8516 55.8934 119.4446 29 1.9498 -0.3914 -0.3608 1.6188 -1.3139 1.3805 0.1151 -0.2314 0.0007 0.1108 -0.012 0.1173 -0.0748 -0.113 0.0013 0.1635 0.0027 0.0029 0.1194 0.0595 0.1602 60.1483 49.8345 141.1325 30 0.2371 -0.068 -0.0186 0.0223 0.0132 0.0594 -0.0342 -0.6752 -0.934 0.0777 0.7321 -1.1294 0.1376 1.7608 -0.0036 0.6733 0.119 -0.0842 1.1757 0.0593 0.9953 87.2347 36.0638 122.5936 31 0.3652 -0.3707 0.0327 1.029 -0.4101 1.2962 -0.0825 0.2672 -1.0755 -0.3451 -0.1637 0.3215 0.6294 0.1128 -0.0008 0.3649 0.1264 0.1537 0.1524 0.0116 0.3876 69.6596 37.6604 117.3813 32 1.3657 -0.9107 1.795 0.9959 -1.0393 2.4179 0.0368 -1.3319 -0.2096 0.7061 0.1496 1.0368 0.0404 -1.1139 0.0673 0.2646 -0.0454 0.0755 0.3655 -0.0142 0.4074 50.0808 49.7144 112.9883 33 0.3053 0.4169 -0.3878 0.5552 -0.5284 0.494 -0.6912 -0.0993 -1.0282 -0.262 0.376 -0.0669 0.7835 0.2615 0.0012 0.3678 0.0793 0.1261 0.3406 -0.0432 0.5004 71.9018 42.7926 112.3282 34 0.0407 -0.0183 -0.0157 0.0533 -0.0102 0.012 -0.4397 -0.1424 0.3322 -0.849 0.6772 -0.3949 0.1693 0.9418 -0.0042 1.4639 0.4015 0.3825 1.218 -0.1328 0.8726 78.2829 36.9036 103.3524 35 0.0141 -0.0094 -0.0218 0.009 0.0317 0.1135 -0.0797 -0.3969 -0.1828 0.1582 0.2979 0.5972 -0.0244 -0.4898 -0.0043 1.7975 0.5225 0.7788 1.7275 -0.7759 2.049 86.4225 30.7444 97.4558 36 0.0991 0.0575 -0.0993 0.2256 0.0336 0.1418 -1.196 -0.1373 -0.4821 -0.6047 -0.1045 -0.099 -0.0243 0.7744 -0.0132 1.5374 -0.4233 0.5301 1.3355 -1.0887 1.363 80.4491 26.9856 103.9181 37 1.6102 0.5243 -0.5096 0.7688 -0.4258 2.6629 -0.0336 0.1806 -0.4342 -0.0162 -0.0435 0.1626 0.7455 -0.3798 0.0482 0.4298 0.0191 0.0612 0.0164 -0.0443 0.3681 59.8826 34.8279 113.7792 38 0.144 -0.0179 0.0618 0.0272 -0.0484 0.099 0.364 1.2311 0.1871 -1.3574 -0.5067 -1.405 0.0423 1.2499 0.0014 0.473 0.1317 0.156 0.5115 0.0827 0.5164 77.7446 52.0028 102.692 39 1.518 0.3349 -0.0846 0.5539 0.0554 2.1056 -0.0727 0.2078 -0.4297 -0.0519 -0.0089 0.1429 0.756 -0.2818 0.1266 0.3927 0.036 0.1037 0.0588 -0.095 0.3291 58.99 35.185 112.3325 40 0.0269 0.0202 -0.0122 0.0738 -0.0552 0.0421 -0.368 0.0234 -0.9296 -0.9458 -0.5843 -0.7213 1.1743 0.6033 0.0021 0.8697 0.1794 0.1132 1.0514 -0.1366 0.7113 79.5586 42.775 87.0646 41 0.2742 0.2964 -0.009 0.4052 0.1049 0.1566 0.2049 0.5098 0.4696 -0.0339 -0.1219 0.1947 0.0981 -0.3031 -0.0064 1.6777 -0.0913 1.8654 1.0818 -0.3116 2.1899 81.516 48.6927 74.9963 42 0.1399 -0.487 -0.0495 3.5713 0.061 0.0246 0.7867 0.6312 0.2738 -0.6303 -0.4606 -1.0712 0.4608 -0.1202 -0.0175 0.705 0.0058 0.3683 0.8544 -0.1274 0.3505 73.4896 48.9249 80.4802 43 0.1716 0.0783 -0.1736 0.0334 -0.0851 0.1673 0.0879 0.3816 0.3249 -0.3933 0.1153 -0.0734 -0.1143 -0.0512 0.0001 0.3044 -0.0119 0.0135 0.3174 -0.0721 0.2396 57.8689 51.083 96.2023 44 0.4138 -0.2544 0.4279 2.2311 0.243 0.5428 -0.095 0.2989 -0.2927 -0.1672 0.0893 -0.028 0.4088 0.0224 -0.0001 0.2298 -0.0213 0.0017 0.3184 -0.0438 0.2592 57.0983 57.928 100.6345 45 0.0537 0.0373 -0.0195 0.1972 0.1415 0.1625 -0.9785 0.2458 -1.0779 -0.1385 -0.5694 -0.3404 -1.8237 0.4339 -0.0046 0.9795 -0.2861 0.175 1.3701 0.2805 1.4247 74.9701 63.3147 78.9968 46 0.8213 -0.4015 -0.129 0.5096 -0.1819 0.5973 -0.5244 0.5651 1.2513 -1.3973 -1.1195 -2.7887 -0.8714 0.7844 -0.0251 0.8181 -0.1194 0.1189 1.2018 0.1595 0.8221 70.2595 59.9856 73.4564 47 1.1838 0.0939 0.2856 1.682 0.1906 1.854 0.0136 0.4466 -0.1429 -0.2419 -0.0225 0.0976 0.1683 -0.0769 0.0049 0.174 -0.0117 0.0228 0.2446 -0.0949 0.0752 55.9561 56.3512 92.468 48 0.028 0.0082 0.0417 0.0812 -0.0394 0.0918 -0.74 0.1846 -1.481 -0.3606 0.804 -1.079 0.581 0.3822 -0.0023 0.6101 -0.0533 -0.0444 0.8785 -0.1074 0.6597 41.6885 37.9958 89.9048 49 1.8656 -0.4484 -0.5647 1.4563 -0.606 1.5591 0.1662 0.8813 -0.7128 -0.1099 0.0369 0.6406 0.409 -0.6392 0.2183 0.2144 -0.0364 -0.0846 0.3953 -0.0941 -0.0866 46.9413 54.5362 86.1355 50 0.0732 -0.0299 -0.0796 0.0899 0.0815 0.2247 -0.1485 0.8439 -0.8122 -1.4786 0.3297 -0.3539 -0.3372 -0.0764 -0.0029 0.8695 0.0902 0.0549 0.8264 0.2512 0.7811 72.9939 80.301 83.818
Refinement TLS group Show large table (6 x 50) 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 22:31)A22 - 31 2 X-RAY DIFFRACTION 2 (chain A and resid 32:58)A32 - 58 3 X-RAY DIFFRACTION 3 (chain A and resid 59:90)A59 - 90 4 X-RAY DIFFRACTION 4 (chain A and resid 91:99)A91 - 99 5 X-RAY DIFFRACTION 5 (chain A and resid 100:106)A100 - 106 6 X-RAY DIFFRACTION 6 (chain A and resid 107:113)A107 - 113 7 X-RAY DIFFRACTION 7 (chain A and resid 114:178)A114 - 178 8 X-RAY DIFFRACTION 8 (chain A and resid 179:185)A179 - 185 9 X-RAY DIFFRACTION 9 (chain A and resid 186:263)A186 - 263 10 X-RAY DIFFRACTION 10 (chain A and resid 264:278)A264 - 278 11 X-RAY DIFFRACTION 11 (chain B and resid 24:31)B24 - 31 12 X-RAY DIFFRACTION 12 (chain B and resid 32:58)B32 - 58 13 X-RAY DIFFRACTION 13 (chain B and resid 59:88)B59 - 88 14 X-RAY DIFFRACTION 14 (chain B and resid 89:94)B89 - 94 15 X-RAY DIFFRACTION 15 (chain B and