Software | Name | Version | Classification |
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PHENIX | 1.17.1_3660refinementPDB_EXTRACT | 3.25 | data extractionHKL-2000 | v708cdata reductionHKL-2000 | v708cdata scalingPHENIX | 1.17.1_3660phasing | | | | | | | | |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4RZD Resolution: 2.75→44.05 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2233 | 1569 | 9.97 % |
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Rwork | 0.2081 | 14175 | - |
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obs | 0.2097 | 15744 | 99.13 % |
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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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Displacement parameters | Biso max: 191.25 Å2 / Biso mean: 85.9 Å2 / Biso min: 35.18 Å2 |
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Refinement step | Cycle: final / Resolution: 2.75→44.05 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 2035 | 22 | 9 | 2066 |
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Biso mean | - | - | 65.74 | 57.65 | - |
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Num. residues | - | - | - | - | 95 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2284 | X-RAY DIFFRACTION | f_angle_d0.84 | 3555 | X-RAY DIFFRACTION | f_dihedral_angle_d13.787 | 1137 | X-RAY DIFFRACTION | f_chiral_restr0.036 | 474 | X-RAY DIFFRACTION | f_plane_restr0.007 | 96 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.75-2.84 | 0.4292 | 140 | 0.4061 | 1244 | 1384 | 99 | 2.84-2.94 | 0.3654 | 141 | 0.3685 | 1238 | 1379 | 99 | 2.94-3.06 | 0.3135 | 146 | 0.2825 | 1249 | 1395 | 99 | 3.06-3.2 | 0.2373 | 129 | 0.2284 | 1261 | 1390 | 99 | 3.2-3.36 | 0.221 | 141 | 0.2164 | 1264 | 1405 | 99 | 3.36-3.57 | 0.2505 | 141 | 0.2153 | 1251 | 1392 | 99 | 3.57-3.85 | 0.1972 | 143 | 0.1816 | 1288 | 1431 | 99 | 3.85-4.24 | 0.1848 | 139 | 0.1701 | 1291 | 1430 | 100 | 4.24-4.85 | 0.2112 | 139 | 0.1753 | 1319 | 1458 | 100 | 4.85-6.11 | 0.1674 | 149 | 0.1816 | 1347 | 1496 | 100 | 6.11-44.05 | 0.223 | 161 | 0.1968 | 1423 | 1584 | 98 |
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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 | 0.1332 | -0.1031 | -0.0917 | 0.1579 | 0.1083 | 0.0808 | 0.3629 | -0.7415 | -0.9172 | 0.3673 | 0.1288 | 0.9174 | 0.5646 | -1.232 | -0.0003 | 0.8818 | 0.1914 | -0.0755 | 0.9597 | 0.1228 | 1.3132 | -4.3181 | 58.3368 | 100.7618 | 2 | 0.1714 | -0.0835 | -0.091 | 0.4464 | -0.009 | 0.1013 | -0.4776 | 0.6588 | 0.2054 | -0.0327 | 0.0974 | 0.2927 | 0.3508 | 0.3495 | -0.0006 | 0.7271 | 0.1564 | -0.0384 | 0.7311 | -0.0578 | 0.6054 | 9.8115 | 52.8007 | 98.3401 | 3 | 0.285 | -0.1799 | -0.0224 | 0.1202 | 0.0496 | 0.1672 | 0.4763 | 0.7098 | -0.6611 | -0.2298 | -0.1778 | 0.2403 | 1.062 | 0.7911 | 0.0085 | 1.0127 | 0.227 | -0.1316 | 0.6355 | -0.0591 | 0.8461 | 14.7846 | 48.0768 | 111.9935 | 4 | 2.2102 | -0.7056 | 2.1011 | 0.5037 | 0.1738 | 4.5543 | -0.4566 | -1.1942 | -0.8595 | 1.8049 | 0.4986 | -0.5641 | 0.2844 | -1.0839 | 0.1939 | 1.1905 | 0.2422 | 0.0464 | 0.753 | -0.0093 | 1.3676 | 13.1005 | 33.5723 | 110.6092 | 5 | 0.9317 | -0.3042 | -0.3428 | 0.7698 | 0.6749 | 0.8167 | -0.2097 | 0.12 | -0.14 | -0.6035 | 0.2559 | 1.0848 | 0.2028 | -0.3113 | -0.0028 | 0.6447 | 0.2702 | 0.0133 | 0.5384 | 0.0625 | 0.7947 | 28.5772 | 34.4368 | 103.7958 | 6 | 0.1872 | -0.2391 | -0.0976 | 0.319 | 0.1153 | 0.0532 | 0.8839 | 0.43 | 1.4664 | -0.7377 | 0.0074 | 0.5801 | 0.0118 | 0.1224 | 0.0027 | 0.9933 | 0.0433 | 0.1025 | 0.6983 | 0.1093 | 0.8149 | 39.9712 | 44.4282 | 95.6157 | 7 | 0.4646 | 0.1299 | -0.2935 | 0.1879 | -0.0576 | 0.4686 | -0.3705 | -0.8521 | -0.5045 | 0.9109 | 0.1882 | 0.1048 | -0.8593 | 1.3723 | -0.0009 | 0.8098 | 0.1316 | -0.1564 | 1.0045 | 0.1281 | 0.8705 | 50.9073 | 31.9928 | 92.1649 | 8 | 0.2424 | 0.2302 | 0.0037 | 0.3323 | 0.1597 | 0.2127 | -0.5023 | -0.8682 | -0.7908 | 0.115 | 0.2554 | -0.8626 | 0.3756 | 1.1785 | -0.0084 | 1.015 | 0.1774 | -0.2001 | 1.3748 | 0.2712 | 1.8216 | 67.1628 | 25.9114 | 90.887 | 9 | 1.4338 | 1.2561 | 0.7046 | 1.2422 | 0.385 | 0.6971 | 0.1719 | 0.1464 | 1.4717 | 0.5869 | 0.202 | 0.41 | -0.8541 | -1.5836 | 0.0106 | 1.1508 | -0.0138 | 0.2108 | 0.8802 | 0.0007 | 0.7825 | 36.6574 | 39.0231 | 122.5312 | 10 | 0.5794 | -0.4624 | -0.359 | 0.5651 | 0.1044 | 0.3878 | 0.3122 | -0.0685 | -0.1562 | -0.4389 | 0.1141 | -0.0531 | -0.4524 | 0.389 | 0.0011 | 0.7516 | 0.1872 | 0.0062 | 0.6827 | 0.0367 | 0.5352 | 39.0612 | 28.6523 | 107.0918 | 11 | 0.6076 | -0.0058 | -0.119 | 0.1273 | 0.1405 | 0.171 | 0.3197 | -0.0594 | 0.2459 | 0.1285 | 0.0209 | -0.1738 | 0.0849 | 0.6578 | 0.0002 | 0.8637 | 0.065 | -0.0313 | 0.888 | 0.0926 | 0.6331 | 41.2226 | 36.2468 | 99.3037 | 12 | 0.1157 | 0.0923 | -0.0658 | 0.068 | -0.0575 | 0.2945 | -0.567 | -0.4033 | 0.6967 | -0.4894 | 0.5597 | 0.4424 | -0.0641 | 0.4864 | 0.0034 | 0.7442 | 0.1065 | 0.0828 | 0.5543 | -0.0084 | 0.6834 | 33.0549 | 36.5747 | 111.156 | 13 | 0.6017 | -0.356 | -0.0796 | 0.5505 | 0.1158 | 0.0234 | 0.1934 | -0.2777 | 0.6521 | 0.336 | 0.4153 | 0.2521 | -0.4811 | 0.138 | -0.0019 | 0.9408 | 0.1202 | 0.1662 | 0.6466 | -0.0954 | 0.7394 | 34.939 | 31.7207 | 126.2997 | 14 | 0.6267 | -0.7112 | 0.4974 | 0.8069 | -0.5635 | 0.394 | 0.7519 | -1.63 | -0.7041 | 0.2223 | 0.8001 | 1.312 | 0.2675 | -0.0064 | 0.0268 | 1.4376 | 0.1317 | 0.185 | 1.4806 | 0.3628 | 1.0744 | 23.7309 | 31.0576 | 142.09 | 15 | 0.4205 | 0.166 | -0.0748 | 0.1661 | 0.1169 | 0.2241 | 0.3028 | -1.2413 | 0.7133 | -0.3479 | 1.0863 | 1.3168 | -1.0351 | -1.2609 | 0.0021 | 1.6548 | 0.1593 | 0.2181 | 2.2068 | 0.1315 | 1.3683 | 30.5809 | 29.9275 | 151.2861 | 16 | 0.2272 | 0.1225 | -0.2198 | 0.1631 | -0.2804 | 0.4784 | -0.2396 | -0.4447 | 0.6519 | -0.6379 | -0.1847 | -0.0692 | -1.4885 | -2.2031 | 0.0027 | 1.3663 | 0.1259 | 0.0164 | 1.4983 | -0.0131 | 0.8833 | 35.2556 | 29.0617 | 144.0676 | 17 | 0.1621 | 0.0281 | 0.0188 | 0.0133 | -0.0006 | 0.0028 | 1.1947 | 0.9568 | -1.3166 | 0.3238 | -0.4811 | 0.9691 | -0.0104 | 1.0318 | 0.0042 | 1.1999 | -0.0105 | 0.045 | 0.9829 | 0.0608 | 1.0662 | 24.8785 | 31.147 | 131.7613 | 18 | 0.3142 | 0.2757 | 0.0873 | 0.2403 | 0.08 | 0.0702 | 0.3306 | -0.0315 | 0.1187 | 0.3195 | -0.4839 | 0.8807 | -0.2288 | 0.6112 | 0.0017 | 0.898 | 0.2245 | 0.0415 | 0.7774 | 0.1028 | 0.9102 | 24.1698 | 38.8308 | 111.6481 | 19 | 0.8266 | -0.8761 | -0.7753 | 1.1786 | 0.9691 | 0.8126 | -0.2667 | 1.3218 | -0.9274 | 0.8563 | -0.3527 | 0.2689 | 0.6274 | 0.0723 | -0.0121 | 0.9122 | 0.3016 | -0.1493 | 0.8356 | -0.1736 | 0.9907 | 9.9148 | 41.0844 | 103.9107 | 20 | 0.786 | -0.0315 | -0.3862 | 0.5634 | 0.2339 | 0.2718 | 0.1653 | 0.1884 | 0.1887 | -0.28 | -0.2631 | 0.9302 | 0.0343 | -0.3418 | -0.0002 | 1.0098 | 0.2378 | -0.059 | 0.5831 | 0.012 | 0.8077 | 6.3355 | 59.6637 | 105.8743 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | (chain A and resid 67:70)A67 - 70 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 71:74)A71 - 74 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 75:78)A75 - 78 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 79:83)A79 - 83 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 84:87)A84 - 87 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 88:91)A88 - 91 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 92:95)A92 - 95 | 8 | X-RAY DIFFRACTION | 8 | (chain A and resid 96:101)A96 - 101 | 9 | X-RAY DIFFRACTION | 9 | (chain A and resid 1:4)A1 - 4 | 10 | X-RAY DIFFRACTION | 10 | (chain A and resid 5:9)A5 - 9 | 11 | X-RAY DIFFRACTION | 11 | (chain A and resid 10:14)A10 - 14 | 12 | X-RAY DIFFRACTION | 12 | (chain A and resid 15:18)A15 - 18 | 13 | X-RAY DIFFRACTION | 13 | (chain A and resid 19:26)A19 - 26 | 14 | X-RAY DIFFRACTION | 14 | (chain A and resid 27:30)A27 - 30 | 15 | X-RAY DIFFRACTION | 15 | (chain A and | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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