Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementHKL-2000 | | data processing | | |
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Refinement | Resolution: 2.3→29.137 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.36 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2422 | 1991 | 3.27 % |
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Rwork | 0.187 | - | - |
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obs | 0.1888 | 60870 | 99.81 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.137 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 8768 | 0 | 0 | 364 | 9132 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 8992 | X-RAY DIFFRACTION | f_angle_d1.158 | 12262 | X-RAY DIFFRACTION | f_dihedral_angle_d14.363 | 3162 | X-RAY DIFFRACTION | f_chiral_restr0.045 | 1385 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1555 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.3-2.3575 | 0.3461 | 141 | 0.2771 | 4190 | X-RAY DIFFRACTION | 100 | 2.3575-2.4212 | 0.3407 | 142 | 0.2608 | 4160 | X-RAY DIFFRACTION | 100 | 2.4212-2.4924 | 0.3468 | 141 | 0.2505 | 4206 | X-RAY DIFFRACTION | 100 | 2.4924-2.5728 | 0.2933 | 142 | 0.2371 | 4190 | X-RAY DIFFRACTION | 100 | 2.5728-2.6647 | 0.2473 | 141 | 0.2238 | 4160 | X-RAY DIFFRACTION | 100 | 2.6647-2.7713 | 0.2781 | 141 | 0.2096 | 4201 | X-RAY DIFFRACTION | 100 | 2.7713-2.8973 | 0.2773 | 142 | 0.2019 | 4163 | X-RAY DIFFRACTION | 100 | 2.8973-3.0499 | 0.2532 | 142 | 0.1912 | 4214 | X-RAY DIFFRACTION | 100 | 3.0499-3.2408 | 0.2395 | 142 | 0.1805 | 4195 | X-RAY DIFFRACTION | 100 | 3.2408-3.4906 | 0.2115 | 142 | 0.1732 | 4197 | X-RAY DIFFRACTION | 100 | 3.4906-3.8412 | 0.2231 | 143 | 0.1746 | 4230 | X-RAY DIFFRACTION | 100 | 3.8412-4.3954 | 0.2177 | 144 | 0.154 | 4236 | X-RAY DIFFRACTION | 100 | 4.3954-5.5316 | 0.1854 | 142 | 0.1521 | 4218 | X-RAY DIFFRACTION | 100 | 5.5316-29.1389 | 0.2511 | 146 | 0.1837 | 4319 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 1.5032 | -0.3147 | -0.375 | 2.7753 | 0.2256 | 2.0129 | 0.012 | 0.2012 | 0.2705 | 0.0084 | 0.019 | 0.1956 | -0.0497 | -0.1052 | -0.0531 | 0.2341 | -0.0247 | -0.0235 | 0.4667 | 0.1359 | 0.3317 | -9.8689 | -10.5728 | 23.9408 | 2 | 2.8173 | 1.2347 | 1.716 | 2.2897 | 0.6423 | 5.7239 | -0.019 | 0.2643 | 0.8402 | -0.1056 | 0.0268 | 0.3811 | -0.5042 | -0.8218 | 0.0175 | 0.3152 | 0.0118 | -0.0084 | 0.4864 | 0.2117 | 0.6669 | -11.4178 | 0.4078 | 20.8758 | 3 | 2.2243 | 0.1669 | 0.1473 | 1.4397 | -0.7123 | 1.3226 | -0.0972 | 0.599 | 0.1244 | -0.1899 | 0.1453 | 0.2214 | 0.0395 | -0.3069 | -0.0499 | 0.2129 | -0.0527 | -0.0281 | 0.4696 | 0.0705 | 0.2748 | -8.4642 | -16.2366 | 21.1269 | 4 | 2.989 | 1.8596 | -1.2014 | 6.5645 | -0.2889 | 0.4775 | 0.1096 | 1.1662 | -0.1244 | 0.0447 | -0.2255 | -0.0563 | -0.6046 | -0.027 | 0.0597 | 0.2303 | 0.0375 | -0.0252 | 0.6141 | 0.1128 | 0.3439 | -3.2397 | -6.8221 | 18.2655 | 5 | 8.8721 | 3.881 | -1.0812 | 9.9723 | -1.1933 | 8.0353 | 0.0538 | -1.0421 | 1.1754 | 0.052 | 0.1627 | 0.6552 | -0.9814 | 0.3353 | -0.1352 | 0.3766 | -0.0713 | 0.0114 | 0.2653 | -0.0931 | 0.3873 | 9.9823 | -2.5264 | 37.5685 | 6 | 1.4476 | -0.162 | -0.6027 | 1.7008 | 0.7111 | 1.9903 | 0.0419 | 0.2098 | 0.2495 | -0.185 | 0.0318 | -0.3106 | 0.0481 | 0.3721 | -0.0675 | 0.2679 | -0.0119 | -0.0001 | 0.5748 | 0.1059 | 0.3094 | 17.7549 | -14.25 | 21.8053 | 7 | 7.3294 | -0.5496 | 0.2275 | 2.1764 | 0.6663 | 0.8112 | 0.0461 | 0.338 | 0.9139 | -0.0089 | 0.0539 | -0.5855 | -0.7488 | 0.5724 | -0.1378 | 0.4947 | -0.1965 | 0.0186 | 0.4031 | 0.0223 | 0.5635 | 17.3884 | -1.1182 | 29.9095 | 8 | 2.4648 | -2.5525 | -1.9309 | 5.7198 | 2.5462 | 3.9215 | -0.3527 | -0.6153 | 0.0222 | 0.5614 | 0.3518 | -0.4056 | 0.1467 | 0.5661 | -0.0314 | 0.2613 | 0.0196 | -0.0699 | 0.6282 | 0.0373 | 0.2951 | 19.6326 | -13.7048 | 37.8504 | 9 | 1.5515 | -0.759 | -0.3767 | 1.3151 | -0.6158 | 1.5745 | -0.1055 | -0.106 | 0.0938 | -0.0553 | -0.0846 | -0.1942 | 0.0122 | 0.555 | 0.169 | 0.2036 | -0.0392 | -0.0108 | 0.488 | 0.0855 | 0.2639 | 13.4106 | -16.7739 | 23.111 | 10 | 3.4886 | 0.8982 | -4.387 | 1.6166 | 0.7874 | 7.959 | -0.1511 | -0.0958 | 0.1389 | 0.1255 | 0.0889 | -0.1914 | 0.3571 | -0.3657 | -0.0634 | 0.2124 | -0.067 | -0.0493 | 0.371 | 0.0634 | 0.2894 | 8.9198 | -11.7651 | 31.5365 | 11 | 1.8589 | 1.5417 | -1.399 | 3.9966 | -0.8654 | 1.6856 | -0.1832 | -0.6474 | -0.5082 | 0.1977 | -0.2022 | -0.7674 | 0.3543 | 0.5898 | 0.361 | 0.3083 | 0.1107 | 0.0278 | 0.5912 | 0.1949 | 0.4746 | -0.5612 | -40.0612 | 48.4651 | 12 | 4.3415 | 1.7602 | -2.3501 | 4.5578 | -3.1691 | 5.0641 | 0.1877 | -0.087 | -0.1383 | -0.701 | -0.4405 | 0.2045 | 0.5748 | 0.8634 | 0.1691 | 0.2933 | 0.022 | -0.0081 | 0.2753 | 0.0247 | 0.2862 | -6.4427 | -30.8885 | 40.4392 | 13 | 4.0218 | 2.0015 | -1.4857 | 3.7176 | -2.2659 | 2.6106 | -0.0877 | 0.1731 | -0.1818 | -0.2993 | -0.1116 | -0.0965 | 0.802 | 0.0724 | 0.0905 | 0.5682 | 0.0676 | 0.0174 | 0.2866 | 0.1092 | 0.4099 | -24.8535 | -58.3009 | 64.8202 | 14 | 5.5028 | -0.2669 | 0.7041 | 2.3821 | -0.3167 | 2.3477 | 0.2136 | 0.119 | -0.466 | 0.0977 | -0.1664 | 0.1091 | 0.6563 | -0.088 | -0.0187 | 0.6907 | -0.007 | 0.0275 | 0.337 | 0.0811 | 0.4196 | -28.6443 | -60.1106 | 65.4075 | 15 | 6.0388 | 4.0472 | -2.0447 | 6.0455 | -0.1991 | 1.1895 | 0.4117 | -0.9161 | 0.6023 | 0.233 | -0.4545 | 0.4776 | -0.3684 | -0.3742 | -0.0898 | 0.305 | 0.0497 | 0.0417 | 0.3643 | -0.0063 | 0.3078 | -24.6635 | -24.8352 | 54.5284 | 16 | 4.64 | 0.0049 | -0.6781 | 3.3973 | -0.7719 | 4.2095 | 0.1205 | -0.3085 | 0.3746 | 0.0325 | 0.0196 | 0.1064 | -0.2627 | 0.0678 | -0.1165 | 0.2178 | 0.0093 | 0.0264 | 0.3033 | 0.032 | 0.2968 | -15.8053 | -21.4304 | 46.8804 | 17 | 4.862 | 2.6643 | -1.1914 | 2.7577 | -0.9297 | 2.3462 | 0.0864 | -0.0228 | 0.0418 | 0.036 | -0.1061 | -0.0388 | -0.0038 | 0.4256 | 0.0156 | 0.2902 | 0.0212 | 0.0036 | 0.3158 | 0.0558 | 0.2888 | -14.1143 | -27.0415 | 49.3961 | 18 | 3.1647 | 0.8251 | -1.7664 | 1.0605 | 0.2053 | 2.9326 | 0.3183 | -0.343 | -0.4732 | -0.134 | 0.499 | 0.9049 | 1.189 | -0.1143 | -0.7547 | 0.6227 | 0.025 | -0.032 | 0.2162 | -0.0226 | 0.3409 | -32.6298 | -46.9043 | 69.8671 | 19 | 2.7062 | -1.3577 | -0.416 | 2.5204 | -2.0978 | 3.5189 | 0.002 | 0.1906 | 0.1774 | 0.2796 | -0.2022 | -0.2534 | 0.0928 | 0.2596 | 0.2271 | 0.4031 | -0.0126 | -0.0354 | 0.244 | 0.0982 | 0.386 | -26.0278 | -45.2699 | 68.2459 | 20 | 4.9215 | -3.0078 | 4.0306 | 7.4924 | -5.0198 | 2.9949 | -0.3183 | -0.5591 | 0.2503 | 0.2423 | -0.0655 | -0.312 | 0.0223 | -0.2963 | 0.4701 | 0.5645 | 0.0883 | 0.0343 | 0.3832 | -0.0119 | 0.2603 | -28.2647 | -43.6362 | 78.6843 | 21 | 0.9992 | 0.0335 | -0.4591 | 1.2028 | -1.1361 | 2.2178 | -0.1098 | 0.6383 | -0.1859 | -0.5938 | 0.1553 | 0.0528 | 0.47 | -0.3938 | -0.0898 | 0.5543 | -0.1763 | -0.0341 | 0.9469 | -0.028 | 0.3451 | 8.0972 | -20.9168 | -9.567 | 22 | 0.8289 | 0.3463 | 0.0223 | 2.3359 | 0.5269 | 1.8478 | 0.2105 | 1.3551 | 0.5044 | -0.3054 | -0.0966 | 0.2319 | -0.2251 | -1.424 | -0.0803 | 0.5211 | 0.0112 | -0.0463 | 1.0926 | 0.1236 | 0.3632 | 6.0002 | -8.9196 | -14.2894 | 23 | 1.7315 | 0.8196 | -1.7505 | 1.6396 | 0.9616 | 3.2858 | -0.2628 | 0.6982 | -0.1699 | -0.6286 | -0.051 | 0.0781 | 0.1033 | -0.8299 | 0.2955 | 0.6177 | -0.1559 | 0.0195 | 0.9974 | 0.0066 | 0.3822 | 9.1194 | -18.1812 | -14.9134 | 24 | 8.606 | 0.31 | 0.0904 | 2.2195 | -0.4223 | 3.4358 | 0.0322 | -1.2607 | -0.6099 | -0.4475 | -0.2324 | -0.4709 | 1.0834 | 0.6546 | 0.1891 | 0.9128 | 0.2283 | 0.1933 | 0.8402 | 0.0773 | 0.4888 | 34.5766 | -17.506 | -37.1755 | 25 | 4.968 | 1.8239 | 2.0801 | 5.8858 | -0.6413 | 4.2943 | 0.1753 | -0.1071 | -1.0496 | -0.8038 | 0.6856 | -0.976 | 0.6141 | -0.4804 | -0.9456 | 1.039 | 0.0046 | 0.1775 | 0.629 | 0.1313 | 0.9854 | 37.5147 | -25.6168 | -36.272 | 26 | 5.2132 | 0.2422 | 0.3633 | 2.1992 | 0.4019 | 2.6681 | 0.3262 | -0.0722 | -0.5428 | -0.0682 | -0.2679 | -0.3979 | 0.4781 | -0.1409 | -0.1528 | 0.9619 | 0.1091 | 0.1533 | 0.7015 | 0.0681 | 0.4815 | 34.0737 | -18.3091 | -34.5094 | 27 | 6.8336 | 0.8628 | 1.4392 | 3.1951 | -0.7118 | 3.4071 | -0.1265 | 0.9333 | -0.0515 | -0.8662 | 0.37 | -0.9077 | 0.3991 | 0.9437 | -0.1201 | 1.3048 | 0.1353 | 0.4445 | 0.9336 | -0.0621 | 0.9095 | 37.1643 | -24.1878 | -45.379 | 28 | 4.9844 | -1.7929 | -1.514 | 2.4838 | 0.8755 | 2.5509 | 0.1496 | -0.0585 | 0.407 | -0.1654 | 0.0449 | -0.2734 | -0.479 | 1.21 | -0.1857 | 0.3583 | -0.0883 | -0.0031 | 1.0006 | 0.2118 | 0.5552 | 31.5732 | -2.3355 | -6.4137 | 29 | 3.3582 | -1.0455 | -1.0583 | 2.0167 | -0.8101 | 2.8252 | 0.4669 | 0.3941 | 0.5909 | -0.7324 | -0.3781 | -0.5187 | -0.378 | 0.192 | -0.0803 | 0.4139 | -0.0522 | 0.0702 | 0.6855 | 0.1946 | 0.421 | 19.0659 | -3.7054 | -3.7186 | 30 | 3.0477 | 0.0054 | -0.2323 | 3.3507 | 1.1378 | 3.3222 | 0.0882 | -0.2146 | -0.0418 | 0.1881 | -0.0404 | -0.0552 | -0.0899 | 0.5226 | -0.0348 | 0.3099 | -0.0965 | 0.0029 | 0.6863 | 0.087 | 0.3483 | 20.5703 | -7.419 | 5.1952 | 31 | 3.0829 | -0.5458 | 0.3734 | 6.7604 | -0.4224 | 2.6926 | -0.105 | 0.2913 | 0.6203 | -0.054 | 0.1663 | -0.0685 | -0.5116 | 0.7679 | -0.0789 | 0.3982 | -0.2209 | -0.0065 | 0.9658 | 0.1956 | 0.5159 | 27.411 | -0.9197 | 2.8837 | 32 | 2.2318 | -5.7403 | -0.2655 | 4.5056 | -1.3963 | 2.585 | 0.0296 | 0.781 | -0.1457 | -0.0096 | -0.333 | 0.0398 | 0.2038 | 0.5613 | 0.3208 | 0.4159 | -0.0395 | 0.0069 | 1.0006 | 0.1634 | 0.4259 | 27.7086 | -9.8275 | -4.1915 | 33 | 4.6647 | -0.374 | -2.4541 | 1.0223 | -0.0777 | 1.7525 | 0.0974 | 0.9367 | 0.7653 | -0.2497 | -0.1369 | -0.0732 | -0.1609 | 0.1897 | -0.0552 | 0.3616 | -0.0154 | -0.0044 | 0.7334 | 0.1914 | 0.3907 | 15.2085 | -4.7409 | -4.1208 | 34 | 1.1763 | 0.4966 | -0.7533 | 2.554 | -0.7198 | 0.5611 | -0.0152 | 0.6051 | -0.0682 | -0.5041 | -0.3721 | -0.4442 | 0.1 | 1.2558 | 0.3899 | 0.5273 | 0.1775 | 0.1971 | 0.8027 | 0.044 | 0.4618 | 40.0671 | -8.6562 | -30.7438 | 35 | 3.6484 | 0.692 | -0.2849 | 2.9653 | 0.8072 | 5.1445 | -0.2711 | -0.9668 | 0.1926 | -0.2696 | -0.1777 | -0.0391 | 0.0307 | 0.5355 | 0.423 | 0.5317 | 0.0785 | 0.045 | 0.6801 | -0.0092 | 0.346 | 31.811 | -6.0028 | -31.3225 | 36 | 2.7325 | 0.6819 | -0.8808 | 1.7409 | 0.7273 | 0.8195 | -0.0115 | -0.2016 | -0.5429 | 0.0453 | 0.0992 | -0.0793 | 0.7692 | 1.0206 | -0.1056 | 0.7338 | 0.1869 | 0.0944 | 1.1596 | 0.1338 | 0.5087 | 34.8211 | -12.8135 | -28.3822 | 37 | 5.7 | -0.7656 | -1.3405 | 6.0416 | -1.1093 | 2.8792 | 0.3696 | -0.7184 | 0.7671 | -0.5862 | 0.1669 | -0.3776 | 0.6963 | -0.3504 | -0.5873 | 0.5801 | 0.0419 | 0.0982 | 0.6168 | -0.0245 | 0.47 | 33.5255 | -0.5225 | -37.0861 | 38 | 4.8198 | 0.8929 | 3.297 | 3.7982 | 1.6466 | 2.0365 | 0.4974 | 0.8608 | 0.24 | -0.6471 | 0.3702 | -0.9231 | -0.087 | 0.9309 | -0.5759 | 0.7963 | 0.0205 | 0.1816 | 0.6105 | 0.1329 | 0.5759 | 39.5994 | -0.5742 | -36.6601 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 459 through 502 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 503 through 527 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 528 through 594 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 595 through 606 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 459 through 469 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 470 through 502 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 503 through 515 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 516 through 533 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 534 through 594 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 595 through 605 )11 | X-RAY DIFFRACTION | 11 | chain 'L' and (resid 1 through 90 )12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 91 through 101 )13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 102 through 155 )14 | X-RAY DIFFRACTION | 14 | chain 'L' and (resid 156 through 212 )15 | X-RAY DIFFRACTION | 15 | chain 'H' and (resid 1 through 22 )16 | X-RAY DIFFRACTION | 16 | chain 'H' | | | | | | | | | | | | | | | |
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