Software | Name | Version | Classification |
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SBC-Collect | | data collectionHKL-3000 | | data collectionHKL-3000 | | phasingSHELXS | | phasingMLPHARE | | phasingDM | | model buildingPHENIX | (phenix.refine: 1.8.2_1309)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.841→31.869 Å / SU ML: 0.14 / Isotropic thermal model: mmixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.55 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.176 | 3217 | 5.06 % | rando |
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Rwork | 0.151 | - | - | - |
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all | 0.152 | 63528 | - | - |
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obs | 0.152 | 63528 | 97.37 % | - |
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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 mean: 25.6 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.841→31.869 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4138 | 0 | 87 | 518 | 4743 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 4558 | X-RAY DIFFRACTION | f_angle_d1.183 | 6163 | X-RAY DIFFRACTION | f_dihedral_angle_d13.994 | 1714 | X-RAY DIFFRACTION | f_chiral_restr0.082 | 710 | X-RAY DIFFRACTION | f_plane_restr0.005 | 810 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection obs | % reflection obs (%) |
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1.8411-1.8686 | 0.2133 | 123 | 0.1978 | 2143 | 2266 | 81 | 1.8686-1.8978 | 0.2116 | 141 | 0.1777 | 2470 | 2611 | 93 | 1.8978-1.9289 | 0.2014 | 142 | 0.1754 | 2519 | 2661 | 96 | 1.9289-1.9622 | 0.2375 | 135 | 0.1698 | 2556 | 2691 | 96 | 1.9622-1.9978 | 0.2258 | 125 | 0.1645 | 2563 | 2688 | 97 | 1.9978-2.0363 | 0.1992 | 135 | 0.1612 | 2654 | 2789 | 99 | 2.0363-2.0778 | 0.2048 | 157 | 0.1568 | 2601 | 2758 | 99 | 2.0778-2.123 | 0.1909 | 136 | 0.1509 | 2657 | 2793 | 99 | 2.123-2.1724 | 0.1716 | 120 | 0.1535 | 2664 | 2784 | 99 | 2.1724-2.2267 | 0.1573 | 116 | 0.1462 | 2680 | 2796 | 100 | 2.2267-2.2869 | 0.1692 | 141 | 0.1433 | 2658 | 2799 | 100 | 2.2869-2.3541 | 0.1733 | 138 | 0.1461 | 2661 | 2799 | 100 | 2.3541-2.4301 | 0.1896 | 150 | 0.1424 | 2643 | 2793 | 99 | 2.4301-2.5169 | 0.163 | 143 | 0.1425 | 2648 | 2791 | 99 | 2.5169-2.6176 | 0.1662 | 128 | 0.1422 | 2676 | 2814 | 99 | 2.6176-2.7367 | 0.182 | 158 | 0.1553 | 2647 | 2815 | 99 | 2.7367-2.8809 | 0.1985 | 153 | 0.1548 | 2656 | 2809 | 99 | 2.8809-3.0613 | 0.19 | 148 | 0.1601 | 2660 | 2808 | 99 | 3.0613-3.2974 | 0.1617 | 139 | 0.1581 | 2668 | 2817 | 99 | 3.2974-3.6288 | 0.1604 | 154 | 0.1407 | 2676 | 2830 | 98 | 3.6288-4.1529 | 0.1504 | 137 | 0.1342 | 2691 | 2828 | 98 | 4.1529-5.2285 | 0.1496 | 144 | 0.1359 | 2715 | 2859 | 98 | 5.2285-31.8735 | 0.1844 | 154 | 0.165 | 2805 | 2959 | 96 |
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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 | 4.0043 | 3.924 | -3.6802 | 6.1101 | -5.0014 | 4.2767 | 0.0211 | 0.217 | 0.0922 | -0.0002 | 0.2372 | 0.3743 | -0.1809 | -0.4924 | -0.2844 | 0.1501 | 0.0588 | -0.0513 | 0.2334 | -0.0376 | 0.1685 | 14.4754 | 48.382 | 5.9144 | 2 | 4.1307 | 0.1819 | 0.4081 | 2.1386 | -0.6495 | 2.0916 | -0.0867 | -0.1328 | -0.1071 | 0.0507 | 0.1197 | 0.1463 | 0.0391 | -0.1771 | -0.0296 | 0.1058 | 0.0334 | -0.0138 | 0.1306 | -0.0193 | 0.1244 | 22.4767 | 35.3488 | 19.1317 | 3 | 3.6146 | 0.0266 | 2.5353 | 3.0236 | -0.0916 | 2.7775 | -0.0988 | -0.1517 | 0.285 | 0.3265 | -0.0757 | -0.0953 | -0.2082 | -0.0514 | 0.1642 | 0.1372 | 0.041 | -0.0105 | 0.1346 | -0.0454 | 0.1702 | 35.7559 | 43.5527 | 21.5612 | 4 | 4.7568 | 1.2252 | 1.7851 | 4.9006 | 2.0832 | 6.2146 | -0.2712 | -0.1893 | 0.7594 | -0.0139 | -0.0723 | 0.0112 | -0.6966 | 0.2165 | 0.2786 | 0.1982 | 0.0693 | -0.0695 | 0.1491 | -0.0196 | 0.2792 | 28.7884 | 49.9186 | 16.7345 | 5 | 3.9763 | -0.5327 | -1.5986 | 3.4161 | 1.2872 | 4.9854 | -0.0404 | 0.1258 | 0.4008 | -0.0137 | -0.1156 | -0.2185 | -0.3892 | 0.323 | 0.117 | 0.1563 | 0.0216 | -0.0708 | 0.1516 | 0.0298 | 0.1945 | 28.4417 | 52.8258 | 12.2638 | 6 | 2.0258 | 0.0036 | -1.7712 | 1.5504 | 2.1393 | 6.0206 | 0.0054 | -0.3702 | 0.3971 | 0.1951 | 0.027 | -0.1022 | -0.5458 | 0.4214 | -0.0476 | 0.3004 | 0.0603 | -0.0673 | 0.2175 | -0.073 | 0.263 | 22.2375 | 57.944 | 22.2747 | 7 | 3.6935 | -0.122 | -0.3367 | 3.1889 | 0.8927 | 3.5347 | -0.0167 | -0.3848 | 0.119 | 0.2895 | -0.0998 | 0.3599 | -0.2196 | -0.3425 | 0.0533 | 0.2757 | 0.1233 | 0.0035 | 0.3184 | -0.1053 | 0.2464 | 12.1025 | 53.5598 | 28.0012 | 8 | 8.4719 | 0.7103 | -1.3849 | 4.7122 | -0.302 | 6.0605 | -0.0142 | -0.5331 | -0.6118 | 0.4803 | -0.0601 | 0.3907 | 0.1421 | -0.3723 | 0.0786 | 0.1869 | 0.0598 | 0.0454 | 0.2599 | 0.0093 | 0.2344 | 13.3866 | 40.2564 | 30.589 | 9 | 7.5661 | -6.8473 | 2.0726 | 7.4699 | -2.0693 | 3.59 | -0.6568 | -0.528 | -0.4227 | 0.8795 | 0.7364 | 0.3992 | 0.0924 | -0.3116 | -0.0953 | 0.2165 | -0.001 | 0.0413 | 0.2323 | 0.0315 | 0.17 | 31.1194 | 22.4912 | 32.3767 | 10 | 6.2209 | 4.435 | -2.3287 | 3.3028 | -1.585 | 6.5424 | 0.012 | -0.0812 | 0.1602 | 0.0752 | -0.0182 | -0.1021 | -0.3726 | 0.1686 | 0.0193 | 0.12 | 0.0274 | -0.0306 | 0.122 | 0.0024 | 0.1414 | 58.0258 | 21.286 | 31.5716 | 11 | 1.7961 | -1.0153 | 0.765 | 2.0157 | -1.0502 | 2.2332 | 0.0228 | -0.0337 | 0.0366 | -0.0179 | -0.0557 | 0.087 | -0.0869 | -0.1327 | 0.027 | 0.0871 | 0.0205 | 0.0023 | 0.0878 | -0.0163 | 0.109 | 39.8298 | 25.6362 | 22.0395 | 12 | 2.558 | -0.9619 | 1.2245 | 1.0672 | 0.3076 | 5.643 | 0.0875 | 0.1433 | 0.0093 | -0.1934 | -0.1309 | -0.0541 | -0.2478 | -0.0932 | 0.049 | 0.1456 | 0.0482 | -0.0066 | 0.0868 | 0.0158 | 0.1633 | 43.7339 | 29.8875 | 14.2508 | 13 | 2.2608 | -0.3774 | 0.0606 | 2.5002 | 1.1834 | 3.668 | 0.0027 | 0.2968 | 0.1301 | -0.1732 | 0.0417 | -0.1822 | -0.4607 | 0.5552 | -0.0574 | 0.1128 | -0.0095 | -0.0015 | 0.1189 | 0.0301 | 0.1385 | 51.1258 | 25.9804 | 14.1586 | 14 | 1.2805 | 0.8127 | 0.3368 | 4.4643 | 1.2204 | 2.3409 | 0.001 | 0.1301 | 0.1169 | -0.1975 | -0.0513 | -0.1311 | -0.1635 | 0.1999 | 0.0479 | 0.0696 | 0.0179 | 0.0058 | 0.1144 | 0.038 | 0.1015 | 55.4124 | 20.0202 | 12.8074 | 15 | 4.8095 | 3.8643 | 1.419 | 7.6199 | 2.2448 | 2.9044 | 0.0553 | 0.2469 | -0.4541 | -0.0635 | 0.1503 | -0.8518 | 0.2417 | 0.4289 | -0.1783 | 0.1095 | 0.0467 | 0.0186 | 0.1601 | -0.0056 | 0.1645 | 59.0639 | 5.509 | 14.5291 | 16 | 3.2083 | 0.7503 | -0.2606 | 3.4956 | 0.2078 | 2.6338 | -0.0098 | 0.0278 | -0.1095 | 0.009 | -0.0378 | 0.232 | 0.1808 | -0.2472 | 0.0408 | 0.0915 | 0 | 0.0046 | 0.0849 | 0.0143 | 0.0909 | 44.0174 | 6.4769 | 21.0376 | 17 | 7.1698 | -6.0599 | -0.9379 | 7.0993 | 0.867 | 3.4959 | 0.1162 | 0.1789 | -0.8656 | -0.0048 | -0.1585 | 0.7712 | 0.0742 | -0.4454 | 0.0532 | 0.1152 | -0.0327 | -0.017 | 0.1711 | -0.0116 | 0.2077 | 23.5632 | 24.8848 | 23.8009 |
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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 -1 through 23 ) | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 24 through 56 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 57 through 98 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 99 through 121 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 122 through 142 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 143 through 179 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 180 through 236 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 237 through 258 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 259 through 281 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 4 through 23 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 24 through 71 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 72 through 98 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 99 through 121 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 122 through 179 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 180 through 193 )16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resid 194 through 258 )17 | X-RAY DIFFRACTION | 17 | chain 'B' | | | | | | | | | | | | | | | |
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