Software | Name | Version | Classification |
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Blu-Ice | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.8.2_1309)refinementMOSFLM | | data reductionSCALA | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.384→56.405 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2159 | 1032 | 5.11 % | random |
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Rwork | 0.1695 | - | - | - |
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all | 0.1718 | - | - | - |
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obs | 0.1718 | 20200 | 99.98 % | - |
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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: 2.384→56.405 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3090 | 0 | 0 | 112 | 3202 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 3172 | X-RAY DIFFRACTION | f_angle_d1.204 | 4293 | X-RAY DIFFRACTION | f_dihedral_angle_d13.909 | 1107 | X-RAY DIFFRACTION | f_chiral_restr0.082 | 440 | X-RAY DIFFRACTION | f_plane_restr0.005 | 563 | | | | | |
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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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2.3842-2.5099 | 0.2785 | 158 | 0.2518 | 2654 | X-RAY DIFFRACTION | 100 | 2.5099-2.6672 | 0.3118 | 136 | 0.2427 | 2673 | X-RAY DIFFRACTION | 100 | 2.6672-2.8731 | 0.2967 | 146 | 0.2254 | 2683 | X-RAY DIFFRACTION | 100 | 2.8731-3.1622 | 0.2433 | 144 | 0.1943 | 2710 | X-RAY DIFFRACTION | 100 | 3.1622-3.6197 | 0.196 | 146 | 0.1582 | 2715 | X-RAY DIFFRACTION | 100 | 3.6197-4.5601 | 0.1666 | 144 | 0.1313 | 2780 | X-RAY DIFFRACTION | 100 | 4.5601-56.4208 | 0.2134 | 158 | 0.1624 | 2953 | 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 | 2.9237 | -0.9191 | -1.9481 | 4.1044 | -2.4895 | 4.271 | 0.1173 | 0.7925 | 0.295 | -0.9705 | -0.2869 | 0.5524 | 0.6061 | -0.6813 | -0.271 | 0.3371 | 0.097 | -0.0592 | 0.2891 | 0.0891 | 0.2919 | -22.8933 | 22.3036 | 42.2691 | 2 | 2.0378 | -3.209 | -1.1907 | 4.6735 | -2.8457 | 2.8352 | -0.382 | 1.065 | -2.3781 | -1.8226 | -0.1903 | 0.6643 | 2.4131 | -0.0631 | -0.6581 | 1.0676 | -0.2025 | -0.0576 | 0.5539 | -0.1625 | 0.5541 | -22.2086 | 7.768 | 40.0892 | 3 | 3.4997 | -0.6104 | 0.7887 | 3.4711 | 0.8491 | 2.9969 | -0.151 | 0.7344 | -0.0296 | -0.5427 | 0.457 | -0.0415 | 0.0049 | 0.5948 | -0.2347 | 0.4643 | -0.0429 | 0.0764 | 0.3759 | 0.0198 | 0.2182 | -17.6605 | 21.7873 | 40.2386 | 4 | 4.4782 | 1.2491 | 1.5332 | 6.6514 | 0.3627 | 3.3893 | -0.3114 | -0.052 | 0.3138 | -0.639 | 0.0946 | -0.0251 | -0.1542 | 0.0455 | -0.2465 | 0.2395 | 0.0322 | 0.043 | 0.1402 | 0.0065 | 0.128 | -14.8214 | 21.4004 | 51.7462 | 5 | 3.0363 | -1.5446 | -0.3866 | 0.8866 | -0.0243 | 4.7595 | -0.2527 | 0.2712 | -1.6898 | -0.7339 | 0.2641 | 2.1525 | 0.8789 | -0.3355 | 0.0481 | 0.4642 | -0.0543 | -0.1401 | 0.2844 | -0.0111 | 0.8636 | -31.834 | 3.9916 | 48.1502 | 6 | 9.4845 | 1.5311 | -7.564 | 7.0971 | -0.9678 | 5.5862 | 0.0221 | 0.3119 | -0.4072 | -0.1243 | 0.55 | -0.5772 | 0.6721 | 0.3364 | -0.2809 | 0.3587 | 0.0657 | -0.0543 | 0.3006 | -0.085 | 0.2914 | -17.7494 | 9.2998 | 52.4379 | 7 | 2.1483 | 1.5177 | -3.134 | 2.2683 | -2.1744 | 4.6424 | -0.4336 | -0.6053 | -1.4833 | -0.8895 | 0.2572 | 3.4825 | 2.3773 | -1.6642 | -0.2967 | 1.1684 | -0.3133 | 0.0462 | 0.575 | 0.21 | 1.8917 | -38.8675 | 5.2709 | 50.6187 | 8 | 2.8099 | 0.3241 | 0.4642 | 3.3609 | 0.8425 | 4.6747 | -0.1399 | 0.0967 | -0.3733 | -0.5308 | 0.1668 | -0.3277 | 0.4979 | 0.5366 | -0.2637 | 0.2999 | 0.0464 | -0.0096 | 0.173 | -0.0159 | 0.2125 | -15.8586 | 15.6712 | 50.9378 | 9 | 2.1008 | -1.0121 | -4.1999 | 8.1916 | 5.1537 | 4.9411 | 0.7425 | 1.3645 | -0.1395 | -2.2891 | 0.3517 | 0.9476 | 0.0889 | -0.6211 | 1.8708 | 0.6074 | -0.2603 | -0.2951 | 0.3472 | 0.0074 | 0.7103 | -30.3259 | 10.1099 | 42.1019 | 10 | 5.0752 | 1.9178 | -2.5553 | 4.0043 | -0.9601 | 2.2363 | -0.1173 | 0.9863 | -0.0639 | -0.468 | 0.3959 | 0.0078 | 0.1143 | -0.0087 | -0.045 | 0.3149 | 0.0584 | 0.0243 | 0.1767 | 0.0439 | 0.2605 | -22.1273 | 23.3152 | 48.9249 | 11 | 1.7463 | -3.4274 | 0.6486 | 6.6633 | -1.158 | 9.0015 | -0.5782 | 1.4677 | 0.4305 | -0.7187 | -0.8031 | 0.2485 | -2.5825 | 0.1506 | -0.3205 | 0.3456 | -0.0139 | -0.0293 | 0.495 | -0.0409 | 0.6828 | -9.891 | 32.2958 | 61.7899 | 12 | 3.2865 | 1.7016 | -0.2123 | 7.6976 | 0.4832 | 1.7424 | 0.0909 | -0.4977 | -0.8221 | 0.3726 | -0.1929 | 0.2375 | 0.6303 | 0.5406 | -0.1893 | 0.4528 | 0.1447 | 0.024 | 0.2726 | 0.09 | 0.4975 | -17.9204 | 11.2289 | 66.5239 | 13 | 9.5491 | 6.7888 | -0.4489 | 4.9861 | -0.144 | 1.5843 | 0.6619 | -1.7485 | -0.8929 | 2.7196 | -0.6164 | 0.5391 | 0.9259 | -1.3156 | -0.0472 | 0.8903 | 0.0007 | 0.181 | 0.632 | 0.2325 | 0.4044 | -26.4807 | 11.413 | 77.0447 | 14 | 1.4881 | -0.2274 | -0.496 | 0.9783 | -0.629 | 2.4881 | -0.6732 | -0.5426 | -0.1588 | 0.6158 | -0.0045 | -0.6391 | 0.1536 | 0.5486 | 0.1026 | 0.3915 | 0.1 | -0.2436 | 0.3277 | -0.0071 | 0.29 | -14.0973 | 17.7271 | 70.817 | 15 | 4.7542 | 3.2716 | -1.3691 | 3.4268 | -0.0164 | 1.5969 | 0.0373 | -0.4215 | -0.039 | 0.4048 | 0.0175 | -0.2372 | 0.1068 | -0.1202 | -0.2282 | 0.2209 | 0.0636 | -0.0551 | 0.2351 | 0.0562 | 0.2302 | -22.3487 | 23.4607 | 66.5734 | 16 | 2.8975 | -0.9536 | -1.5112 | 0.3678 | 0.1627 | 2.2618 | -0.4864 | -0.5131 | -3.9656 | 0.6028 | 0.5868 | 1.157 | 2.3463 | -1.461 | -0.1573 | 0.9043 | -0.2775 | -0.0253 | 0.8887 | 0.0889 | 1.203 | -37.87 | 4.1593 | 69.7829 | 17 | 7.1512 | 2.9867 | 1.0427 | 4.3454 | 1.8468 | 4.7107 | 0.2815 | -0.5378 | 0.3031 | 1.0593 | -0.3972 | 0.9985 | 0.0912 | -0.4162 | -0.173 | 0.5317 | 0.0713 | 0.1312 | 0.3634 | 0.0871 | 0.2573 | -31.8777 | 20.2799 | 71.9529 | 18 | 8.432 | 1.718 | -2.6604 | 3.8838 | 0.4896 | 1.1251 | -1.2486 | 1.0682 | -1.7435 | 0.4923 | -0.0813 | 1.1313 | 1.7128 | -1.0072 | 1.4945 | 1.704 | -0.1977 | -0.0179 | 1.6777 | -0.0906 | 1.5017 | -38.6565 | 2.8753 | 63.1404 | 19 | 5.9425 | 1.1359 | -0.5224 | 0.4255 | -1.1566 | 6.3477 | -0.7061 | -1.2964 | -1.2924 | 0.081 | 0.7716 | -0.5575 | 0.6845 | -0.5674 | -1.1273 | 0.3363 | 0.2115 | 0.058 | -0.7853 | 0.6119 | 0.2555 | -30.7816 | 14.1745 | 62.2973 | 20 | 2.4072 | 0.4378 | 0.1572 | 2.2085 | 0.3971 | 4.9392 | -0.0289 | -0.1569 | -0.1747 | 0.8233 | 0.2549 | 0.0549 | 0.2353 | 0.072 | -0.0788 | 0.292 | 0.1328 | -0.0202 | 0.3265 | 0.012 | 0.174 | -21.9399 | 19.6941 | 67.9164 | 21 | 0.2445 | -0.0905 | 1.0129 | 5.7566 | 0.1971 | 6.3831 | 0.0615 | -0.0912 | 0.0065 | -0.2184 | 0.0954 | 0.766 | -0.1996 | -1.328 | -0.3405 | 0.4357 | 0.161 | 0.0412 | 0.4237 | 0.0973 | 0.3364 | -36.9506 | 32.5008 | 60.5888 | 22 | 6.022 | 2.7913 | 2.2073 | 7.9707 | 4.4789 | 8.7737 | 0.046 | 0.4324 | 0.5796 | 0.4979 | 0.1658 | 0.8083 | -1.1042 | -1.6338 | 0.2365 | 0.2193 | 0.1769 | 0.0928 | 0.622 | 0.1937 | 0.4403 | -41.108 | 33.3979 | 59.4997 | 23 | 3.4632 | -0.7368 | 0.8611 | 0.3324 | 0.4562 | 2.1885 | -0.1177 | -0.0118 | 0.6742 | 0.3372 | 0.4568 | 0.1655 | -0.7323 | -0.438 | -0.2162 | 0.3334 | 0.1491 | 0.0907 | 0.2248 | 0.0687 | 0.379 | -30.5938 | 36.9046 | 56.1141 | 24 | 6.0178 | 4.1487 | 4.371 | 6.4161 | 3.9526 | 7.7616 | -0.5421 | 0.9731 | -2.1313 | -1.1652 | -0.1397 | 1.2557 | 3.178 | -2.9249 | -0.4431 | 0.6565 | -0.4196 | 0.0244 | 1.0766 | -0.1048 | 1.0229 | -46.7611 | 17.6759 | 55.7745 | 25 | 3.2438 | 3.673 | 3.2715 | 5.8968 | 6.0371 | 6.5337 | 0.7049 | 0.7038 | -0.1501 | 0.2202 | -0.0933 | 1.0398 | 1.3825 | -0.8902 | -0.8377 | 0.455 | -0.1094 | -0.2355 | 0.5603 | 0.2095 | 0.514 | -42.8945 | 20.7106 | 49.1308 | 26 | 3.9677 | 1.2854 | 0.4295 | 2.0586 | 1.4589 | 1.091 | -0.5114 | 0.6724 | 0.0336 | -1.8581 | 0.1407 | 0.7062 | -0.2741 | -0.5538 | -0.0092 | 0.4537 | 0.0129 | -0.2246 | 0.3585 | 0.1325 | 0.3182 | -35.9332 | 28.2357 | 45.7399 | 27 | 1.9809 | -4.2957 | -7.0362 | 1.765 | 2.8272 | 4.5888 | -2.4371 | -2.3715 | -1.7848 | 0.0361 | -0.2924 | -0.6657 | 3.0306 | -2.257 | -1.2382 | 2.0622 | -0.4651 | -0.5399 | 1.3264 | 0.5299 | 1.025 | -44.8275 | 11.4325 | 57.7383 | 28 | 4.7348 | -0.0295 | -0.1581 | 2.5746 | 1.2805 | 1.666 | -0.1319 | 0.2136 | 0.4367 | -0.472 | 0.3057 | 0.6095 | -0.2272 | -0.3262 | -0.1103 | 0.3267 | 0.0613 | -0.0702 | 0.3665 | 0.1353 | 0.3238 | -33.6762 | 30.8302 | 49.914 | 29 | 5.0782 | -0.2925 | 4.4612 | 2.1535 | -0.6015 | 4.0301 | -0.6588 | -1.9573 | -0.933 | 1.4832 | 0.2453 | 1.1107 | -0.0413 | -1.3152 | 0.1019 | 0.7655 | 0.1344 | 0.1726 | 0.7509 | 0.2157 | 0.8774 | -43.9069 | 24.8685 | 65.3873 | 30 | 4.0436 | 1.503 | -0.8432 | 7.8908 | -0.5246 | 1.6935 | -0.0093 | 0.0175 | 0.2457 | 0.0394 | 0.1912 | 0.2857 | -0.2979 | -0.2288 | -0.1448 | 0.1752 | 0.0354 | -0.0687 | 0.2468 | -0.0019 | 0.1855 | -28.0257 | 30.4683 | 58.3313 |
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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 7:19)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 20:26)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 27:47)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 48:58)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 59:70)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 71:85)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 86:93)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 94:112)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 113:122)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 123:137)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 4:9)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 10:19)13 | X-RAY DIFFRACTION | 13 | (chain B and resid 20:25)14 | X-RAY DIFFRACTION | 14 | (chain B and resid 26:47)15 | X-RAY DIFFRACTION | 15 | (chain B and resid 48:61)16 | X-RAY DIFFRACTION | 16 | (chain B and resid 62:68)17 | X-RAY DIFFRACTION | 17 | (chain B and resid 69:85)18 | X-RAY DIFFRACTION | 18 | (chain B and | | | | | | | | | | | | | | | | | |
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