Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.292→35.665 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2431 | 2140 | 5.05 % |
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Rwork | 0.1845 | - | - |
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obs | 0.1876 | 42405 | 99.36 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Refinement step | Cycle: LAST / Resolution: 2.292→35.665 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6602 | 0 | 0 | 347 | 6949 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 6772 | X-RAY DIFFRACTION | f_angle_d1.222 | 9208 | X-RAY DIFFRACTION | f_dihedral_angle_d14.224 | 2412 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 1024 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1178 | | | | | |
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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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2.2917-2.345 | 0.3359 | 117 | 0.2489 | 2446 | X-RAY DIFFRACTION | 92 | 2.345-2.4037 | 0.2995 | 146 | 0.2386 | 2656 | X-RAY DIFFRACTION | 100 | 2.4037-2.4687 | 0.3155 | 139 | 0.2319 | 2704 | X-RAY DIFFRACTION | 100 | 2.4687-2.5413 | 0.3466 | 135 | 0.2318 | 2658 | X-RAY DIFFRACTION | 100 | 2.5413-2.6233 | 0.326 | 153 | 0.2355 | 2660 | X-RAY DIFFRACTION | 100 | 2.6233-2.717 | 0.3139 | 144 | 0.2255 | 2690 | X-RAY DIFFRACTION | 100 | 2.717-2.8257 | 0.2976 | 122 | 0.2241 | 2688 | X-RAY DIFFRACTION | 100 | 2.8257-2.9543 | 0.2767 | 148 | 0.2088 | 2688 | X-RAY DIFFRACTION | 100 | 2.9543-3.11 | 0.2726 | 148 | 0.2158 | 2688 | X-RAY DIFFRACTION | 100 | 3.11-3.3047 | 0.2595 | 133 | 0.1956 | 2670 | X-RAY DIFFRACTION | 100 | 3.3047-3.5596 | 0.2381 | 141 | 0.1713 | 2734 | X-RAY DIFFRACTION | 100 | 3.5596-3.9174 | 0.2142 | 164 | 0.1634 | 2677 | X-RAY DIFFRACTION | 100 | 3.9174-4.4834 | 0.1794 | 155 | 0.1407 | 2716 | X-RAY DIFFRACTION | 100 | 4.4834-5.645 | 0.178 | 140 | 0.1348 | 2739 | X-RAY DIFFRACTION | 100 | 5.645-35.669 | 0.2241 | 155 | 0.1763 | 2851 | 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 | 2.8759 | -0.0627 | -0.0972 | 3.241 | 0.3893 | 1.1724 | 0.1458 | 0.2074 | 0.3796 | 0.4573 | 0.0291 | -0.49 | -0.1082 | -0.0509 | -0.0887 | 0.3093 | 0.0597 | -0.0744 | 0.286 | 0.0062 | 0.3281 | 22.127 | 82.2477 | 41.5008 | 2 | 2.9432 | 0.8002 | 0.3618 | 1.8478 | -0.2512 | 1.6641 | 0.0375 | -0.3087 | 0.2863 | -0.1244 | -0.071 | 0.1845 | -0.0074 | -0.0872 | 0.0122 | 0.1904 | 0.0184 | -0.0539 | 0.2242 | -0.019 | 0.1625 | 14.2129 | 91.5658 | 38.0563 | 3 | 1.6113 | 0.8331 | 0.1963 | 3.3352 | 0.1837 | 2.2363 | -0.8946 | -0.2455 | 0.0864 | 0.8478 | -0.1687 | 0.0266 | 1.2995 | -0.2099 | 0.3565 | -0.0531 | 0.1026 | -0.2311 | 0.3129 | -0.0366 | 0.215 | 10.9372 | 88.2906 | 43.8103 | 4 | 1.8272 | -1.6734 | -0.6551 | 1.9964 | 0.3744 | 2.3077 | -0.4728 | -0.1413 | 0.0581 | -0.0597 | 0.1464 | 0.0294 | 0.1497 | -0.006 | 0.2429 | 0.3477 | -0.0077 | -0.0213 | 0.2606 | -0.0023 | 0.2142 | 14.1559 | 81.3832 | 42.5064 | 5 | 0.7999 | -0.4255 | -0.0803 | 3.1207 | -0.8178 | 0.6721 | 0.035 | 0.0425 | 0.1286 | -0.1367 | -0.0995 | -0.0419 | -0.0869 | -0.0058 | 0.108 | 0.2431 | -0.0249 | -0.0498 | 0.208 | -0.0426 | 0.2454 | 14.5055 | 99.1026 | 31.1984 | 6 | 1.2243 | -0.2738 | -0.5599 | 1.2659 | 0.2245 | 0.9471 | -0.1415 | 0.0633 | 0.0627 | 0.1543 | 0.1054 | -0.1114 | -0.0413 | 0.0649 | 0.0101 | 0.1913 | -0.0331 | -0.0581 | 0.2136 | 0.0152 | 0.1887 | 27.611 | 68.284 | 28.8296 | 7 | 1.1167 | -0.292 | -0.185 | 1.7347 | -0.1375 | 0.9419 | -0.0906 | 0.1719 | -0.1214 | 0.0095 | 0.0404 | -0.1954 | -0.0927 | 0.1181 | 0.039 | 0.2678 | -0.1131 | -0.0266 | 0.3464 | -0.0395 | 0.214 | 32.3352 | 65.6841 | 22.4883 | 8 | 1.797 | -1.0695 | -1.9369 | 1.4293 | 0.8327 | 4.1438 | -0.1578 | -0.4433 | -0.4548 | 0.1046 | 0.1606 | -0.459 | 0.1126 | 1.0221 | -0.048 | 0.2374 | -0.0549 | -0.0824 | 0.4513 | -0.0791 | 0.5303 | 40.8457 | 61.2432 | 25.5247 | 9 | 4.0679 | -0.1829 | -3.4561 | 1.7666 | 1.2176 | 3.0962 | 0.1224 | 0.2249 | 0.0452 | -0.5299 | -0.0219 | 0.1483 | -0 | -0.0908 | 0.0236 | 0.4658 | 0.0383 | -0.0268 | 0.261 | 0.077 | 0.2022 | 11.3173 | 86.9501 | 12.7501 | 10 | 1.5743 | -0.4377 | -0.5358 | 1.7959 | 0.2143 | 1.9175 | 0.0314 | 0.0619 | 0.2786 | -0.5182 | -0.0086 | -0.2219 | -0.2279 | -0.0026 | -0.0425 | 0.374 | -0.0043 | -0.0178 | 0.2092 | 0.0569 | 0.3249 | 12.9049 | 95.4084 | 19.033 | 11 | 1.4062 | 0.0062 | 0.1829 | 1.3173 | 0.1404 | 2.0113 | -0.1215 | 0.1033 | 0.1499 | -0.4225 | 0.0429 | -0.1663 | -0.2537 | -0.1002 | 0.0272 | 0.3618 | -0.039 | -0.0058 | 0.1962 | 0.064 | 0.2698 | 12.7862 | 91.555 | 18.8068 | 12 | 0.113 | -0.5136 | -0.3078 | 1.049 | 0.6666 | 0.3311 | 0.3673 | -0.157 | 0.2187 | -0.4455 | -0.0195 | -0.1391 | 0.0532 | -0.0532 | -0.1906 | 0.683 | -0.0738 | 0.1117 | 0.3018 | 0.0119 | 0.2744 | 22.1156 | 77.5987 | 5.9123 | 13 | 0.72 | 0.7878 | -1.04 | 3.3105 | -1.093 | 2.2484 | 0.0246 | 0.1326 | 0.016 | 0.067 | 0.039 | -0.0648 | -0.2897 | 0.2057 | -0.0735 | 0.1958 | -0.0652 | -0.023 | 0.279 | 0.0115 | 0.2057 | 24.9386 | 57.5369 | 14.9656 | 14 | 1.5441 | 1.4538 | 0.2707 | 3.5682 | 0.8066 | 0.4335 | 0.1391 | 0.1615 | -0.0988 | -0.871 | -0.2026 | 0.1012 | -0.2581 | -0.2946 | -0.138 | 0.254 | 0.012 | -0.0517 | 0.2908 | -0.0176 | 0.2209 | 15.9298 | 55.3473 | 16.7002 | 15 | 1.0701 | -0.0655 | -0.1265 | 2.1748 | -0.7859 | 2.2637 | 0.006 | 0.1805 | 0.0738 | 0.1355 | -0.0203 | -0.0178 | -0.3046 | 0.1945 | -0.0117 | 0.1531 | -0.0377 | -0.015 | 0.2504 | -0.0233 | 0.2368 | 23.3411 | 58.071 | 15.0106 | 16 | 1.8665 | -0.2749 | 1.2842 | 4.7362 | -1.33 | 3.8051 | 0.2111 | 0.4084 | -0.1352 | -1.3313 | -0.3424 | 0.0966 | 0.4441 | 0.2843 | 0.2002 | 0.2452 | -0.0509 | 0.0474 | 0.4073 | -0.0265 | 0.1902 | 22.9534 | 54.1293 | 5.671 | 17 | 2.6656 | 0.0634 | 0.3839 | 3.2818 | 0.0625 | 1.3629 | 0.1607 | -0.1803 | -0.0398 | 0.8736 | -0.0015 | 0.4419 | 0.3036 | 0.0234 | -0.1209 | 0.2706 | 0.0634 | 0.0114 | 0.3293 | -0.0336 | 0.1271 | 7.2803 | 38.6962 | 42.9222 | 18 | 1.9855 | 1.4526 | -0.0743 | 2.1059 | 0.3516 | 1.7126 | -0.0441 | -0.1879 | -0.3075 | 0.4084 | -0.0489 | -0.4128 | 0.081 | 0.0206 | 0.0457 | 0.2168 | 0.0308 | -0.0484 | 0.2072 | 0.0127 | 0.1814 | 13.7046 | 29.3613 | 37.6985 | 19 | 1.8751 | 0.4193 | -0.5364 | 4.9834 | -0.1242 | 2.9585 | 0.0739 | 0.0334 | -0.0591 | 0.6131 | 0.204 | -0.3698 | 0.202 | 0.418 | -0.0419 | 0.2648 | 0.011 | -0.1774 | 0.1932 | 0.1089 | 0.3222 | 18.1582 | 32.5571 | 42.4187 | 20 | 0.7231 | -0.5178 | 0.3516 | 1.9243 | -0.0143 | 2.2541 | -0.1993 | -0.3138 | -0.0242 | -0.0027 | 0.2578 | -0.102 | 0.2783 | 0.1338 | -0.0591 | 0.2222 | 0.0659 | -0.0824 | 0.2712 | 0.0105 | 0.2169 | 15.0553 | 39.5011 | 41.998 | 21 | 0.185 | -0.1572 | 0.324 | 2.0917 | 0.4004 | 0.7134 | 0.0174 | -0.1133 | -0.329 | 0.263 | 0.1855 | -0.2969 | 0.1677 | 0.0543 | -0.0543 | 0.177 | -0.0138 | -0.0252 | 0.1679 | 0.0045 | 0.3105 | 11.72 | 21.8418 | 31.1032 | 22 | 1.5893 | 1.3748 | 0.0809 | 3.6747 | 1.5653 | 0.9972 | -0.0948 | -0.3312 | -0.0267 | 0.0905 | 0.0025 | 0.0821 | 0.1714 | 0.1273 | 0.1261 | 0.1933 | 0.0183 | -0.0779 | 0.1976 | 0.0095 | 0.2317 | 6.5766 | 35.1035 | 35.1358 | 23 | 2.7429 | -1.4723 | 1.6758 | 1.6523 | -1.084 | 1.8028 | -0.1535 | -0.085 | 0.426 | 0.174 | -0.1015 | 0.0465 | -0.198 | 0.0099 | 0.1088 | 0.2196 | -0.0573 | -0.0352 | 0.2248 | -0.0098 | 0.1813 | -4.4887 | 61.2037 | 30.5806 | 24 | 1.6491 | 0.1259 | 0.5156 | 1.2486 | 0.3984 | 0.8319 | 0.2226 | 0.2553 | 0.2268 | 0.1678 | -0.1675 | 0.0986 | 0.136 | -0.0887 | -0.0438 | 0.3034 | -0.0088 | 0.0127 | 0.288 | -0.0081 | 0.1322 | -6.7938 | 55.138 | 27.0806 | 25 | 3.292 | -0.0139 | 2.4278 | 1.6058 | -0.1904 | 3.1423 | 0.1373 | -0.6894 | -0.0043 | 0.3467 | 0.1065 | 0.6153 | 0.0345 | -0.7585 | -0.2144 | 0.2287 | 0.0332 | 0.0602 | 0.3193 | 0.0219 | 0.308 | -14.2855 | 59.2352 | 32.1821 | 26 | 4.5898 | -0.7684 | 1.7067 | 1.9344 | -0.9607 | 1.7908 | 0.033 | 0.072 | 0.1297 | -0.5372 | -0.1055 | -0.2088 | 0.1637 | 0.2123 | 0.0433 | 0.1791 | 0.0045 | -0.028 | 0.2746 | -0.007 | 0.2492 | 11.066 | 34.1019 | 12.3515 | 27 | 1.458 | 0.357 | 0.4814 | 1.5129 | -0.2895 | 1.2769 | 0.0618 | 0.0578 | -0.3116 | -0.1495 | -0.0147 | -0.0954 | 0.0562 | -0.0184 | -0.0513 | 0.1841 | 0.0041 | -0.0402 | 0.1923 | -0.0509 | 0.249 | 10.9183 | 25.5863 | 18.8229 | 28 | 1.4811 | -0.6664 | 0.3303 | 1.6792 | -0.2772 | 1.2616 | 0.19 | -0.0716 | -0.2783 | -0.2003 | -0.0148 | 0.0624 | 0.1773 | -0.0178 | -0.1962 | 0.1589 | -0.0309 | -0.0318 | 0.1758 | -0.029 | 0.2592 | 11.0733 | 29.4092 | 18.5997 | 29 | 0.9388 | -1.873 | 0.9133 | 2.8771 | -1.4716 | 0.7108 | 0.2244 | -0.0144 | 0.0718 | 0.0853 | 0.2318 | 0.1635 | 0.1213 | -0.2551 | -0.0813 | 0.2865 | -0.0203 | -0.1239 | 0.2571 | -0.0681 | 0.1611 | -0.953 | 43.5618 | 8.4917 | 30 | 0.5451 | 0.7135 | 0.4296 | 3.2163 | 0.6511 | 1.2887 | 0.0207 | 0.1443 | 0.1006 | 0.1071 | 0.0135 | 0.0538 | -0.0883 | -0.0985 | -0.0189 | 0.211 | 0.0223 | -0.0595 | 0.2564 | 0.0239 | 0.1486 | -1.3386 | 63.3849 | 18.3078 | 31 | 0.9503 | 1.0698 | -0.5182 | 2.8813 | -0.5567 | 0.4158 | -0.2604 | 0.2206 | -0.0062 | -0.2693 | -0.0608 | -0.324 | -0.3012 | -0.051 | 0.1539 | 0.325 | -0.0006 | 0.0155 | 0.3166 | 0.1238 | 0.2351 | 7.8678 | 65.6244 | 17.8083 | 32 | 1.0735 | 0.2361 | 0.4661 | 3.2372 | 0.9322 | 1.2992 | 0.0733 | 0.1803 | 0.0528 | 0.0163 | -0.1086 | 0.1345 | -0.0049 | -0.1684 | 0.0208 | 0.2015 | 0.009 | -0.0322 | 0.2492 | -0.0029 | 0.1854 | 0.0749 | 62.8884 | 17.904 | 33 | 1.293 | 0.2638 | 0.16 | 4.328 | 2.0363 | 2.7021 | -0.1066 | 0.1899 | 0.4649 | -0.885 | -0.0692 | 0.1366 | -0.6959 | -0.2892 | 0.1826 | 0.3592 | 0.0346 | -0.1529 | 0.2916 | 0.0313 | 0.2913 | -1.4287 | 66.9418 | 8.9076 |
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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 'H' and (resid 1 through 17 )2 | X-RAY DIFFRACTION | 2 | chain 'H' and (resid 18 through 60 )3 | X-RAY DIFFRACTION | 3 | chain 'H' and (resid 61 through 76 )4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 77 through 91 )5 | X-RAY DIFFRACTION | 5 | chain 'H' and (resid 92 through 111 )6 | X-RAY DIFFRACTION | 6 | chain 'H' and (resid 112 through 157 )7 | X-RAY DIFFRACTION | 7 | chain 'H' and (resid 158 through 200 )8 | X-RAY DIFFRACTION | 8 | chain 'H' and (resid 201 through 225 )9 | X-RAY DIFFRACTION | 9 | chain 'L' and (resid 1 through 18 )10 | X-RAY DIFFRACTION | 10 | chain 'L' and (resid 19 through 69 )11 | X-RAY DIFFRACTION | 11 | chain 'L' and (resid 70 through 101 )12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 102 through 113 )13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 114 through 150 )14 | X-RAY DIFFRACTION | 14 | chain 'L' and (resid 151 through 163 )15 | X-RAY DIFFRACTION | 15 | chain 'L' and (resid 164 through 197 )16 | X-RAY DIFFRACTION | 16 | chain 'L' | | | | | | | | | | | | | | | |
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