Software | Name | Version | Classification |
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PHENIX | | refinementSCALA | 3.3.16data scalingPHASER | | phasingPDB_EXTRACT | 3.2 | data extractionXDS | | data reduction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 2YFC Resolution: 1.801→43.59 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.65 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2072 | 2917 | 5.08 % |
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Rwork | 0.1633 | 54540 | - |
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obs | 0.1655 | 57457 | 98.95 % |
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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: 108.51 Å2 / Biso mean: 24.3282 Å2 / Biso min: 4.26 Å2 |
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Refinement step | Cycle: final / Resolution: 1.801→43.59 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4270 | 0 | 46 | 909 | 5225 |
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Biso mean | - | - | 11.86 | 34.33 | - |
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Num. residues | - | - | - | - | 559 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 4460 | X-RAY DIFFRACTION | f_angle_d0.792 | 6046 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 675 | X-RAY DIFFRACTION | f_plane_restr0.006 | 816 | X-RAY DIFFRACTION | f_dihedral_angle_d17.601 | 1658 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8013-1.8309 | 0.3296 | 126 | 0.274 | 2428 | 2554 | 94 | 1.8309-1.8624 | 0.2759 | 138 | 0.2267 | 2589 | 2727 | 100 | 1.8624-1.8963 | 0.2889 | 130 | 0.2026 | 2579 | 2709 | 99 | 1.8963-1.9328 | 0.2152 | 151 | 0.1874 | 2585 | 2736 | 100 | 1.9328-1.9722 | 0.2329 | 146 | 0.182 | 2548 | 2694 | 99 | 1.9722-2.0151 | 0.2611 | 135 | 0.1714 | 2605 | 2740 | 100 | 2.0151-2.062 | 0.208 | 141 | 0.1711 | 2567 | 2708 | 99 | 2.062-2.1135 | 0.1942 | 154 | 0.1595 | 2583 | 2737 | 100 | 2.1135-2.1707 | 0.1754 | 138 | 0.1541 | 2566 | 2704 | 99 | 2.1707-2.2346 | 0.198 | 131 | 0.1535 | 2597 | 2728 | 99 | 2.2346-2.3067 | 0.2459 | 131 | 0.1588 | 2601 | 2732 | 100 | 2.3067-2.3891 | 0.208 | 139 | 0.1563 | 2602 | 2741 | 99 | 2.3891-2.4848 | 0.2331 | 138 | 0.1682 | 2593 | 2731 | 100 | 2.4848-2.5978 | 0.2317 | 143 | 0.1677 | 2600 | 2743 | 99 | 2.5978-2.7348 | 0.2139 | 135 | 0.1691 | 2610 | 2745 | 99 | 2.7348-2.9061 | 0.2328 | 137 | 0.1626 | 2625 | 2762 | 99 | 2.9061-3.1304 | 0.2091 | 129 | 0.1586 | 2622 | 2751 | 99 | 3.1304-3.4453 | 0.2004 | 125 | 0.1519 | 2624 | 2749 | 99 | 3.4453-3.9436 | 0.1661 | 139 | 0.144 | 2621 | 2760 | 98 | 3.9436-4.9674 | 0.1592 | 156 | 0.1396 | 2650 | 2806 | 98 | 4.9674-43.6027 | 0.2081 | 155 | 0.1751 | 2745 | 2900 | 97 |
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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 | 0.0279 | 0.0184 | 0.0299 | 0.0076 | 0.0059 | 0.0118 | 0.0502 | -0.0767 | -0.1093 | 0.1103 | -0.1199 | -0.0935 | -0.0185 | 0.0688 | -0 | 0.1296 | -0.025 | -0.0261 | 0.1664 | 0.012 | 0.1013 | -12.5071 | -26.2136 | -14.3002 | 2 | 0.3178 | -0.0875 | -0.0895 | 0.0338 | -0.0294 | 0.1405 | -0.0453 | -0.1645 | 0.3397 | 0.0221 | -0.0386 | 0.1007 | -0.1144 | 0.0439 | -0.0188 | 0.1459 | -0.0568 | -0.0253 | 0.0697 | -0.0421 | 0.1758 | -25.798 | -11.201 | -23.5274 | 3 | 0.2145 | -0.1092 | 0.1384 | 0.0624 | 0.0939 | 0.191 | 0.0515 | -0.0708 | -0.0139 | 0.0035 | -0.0528 | -0.0043 | 0.0806 | -0.0073 | -0.0201 | 0.1146 | -0.0302 | -0.0347 | 0.0818 | 0.0089 | 0.0825 | -28.5689 | -25.9571 | -27.2963 | 4 | 0.0156 | -0.0062 | 0.0112 | 0.0159 | 0.0225 | 0.0557 | 0.0124 | -0.0581 | -0.0522 | 0.0807 | -0.0319 | -0.0228 | -0.044 | -0.0432 | -0.0175 | 0.2017 | -0.0831 | -0.0468 | 0.1834 | 0.0552 | 0.1252 | -24.9137 | -37.7376 | -9.68 | 5 | 0.011 | 0.0002 | 0.0015 | 0.0015 | -0.0081 | 0.0007 | -0.0113 | 0.0459 | 0.0083 | -0.0235 | 0.0336 | 0.089 | -0.0079 | -0.13 | 0 | 0.0977 | -0.0444 | -0.0146 | 0.1731 | -0.0024 | 0.1487 | -69.5439 | -28.9724 | -6.4219 | 6 | 0.0052 | -0.0017 | 0.0011 | 0.0025 | -0.005 | -0.0014 | -0.012 | 0.0902 | 0.0097 | -0.0734 | -0.0533 | 0.0609 | 0.0703 | -0.0307 | 0 | 0.1849 | -0.0042 | -0.0233 | 0.3329 | 0 | 0.2006 | -64.2132 | -27.7721 | -18.8055 | 7 | 0.5218 | 0.118 | -0.1843 | 0.1315 | -0.027 | 0.2174 | -0.2358 | 0.4316 | 0.4955 | -0.0903 | 0.2546 | -0.1027 | -0.0616 | -0.2568 | 0.0123 | 0.0828 | 0.1261 | -0.0612 | -0.0999 | -0.0013 | 0.2405 | -55.1057 | -12.2278 | -2.4468 | 8 | 0.0032 | 0.0038 | 0 | 0.006 | 0.0014 | -0.0004 | 0.004 | -0.0192 | 0.0199 | 0.0329 | 0.0151 | -0.0242 | -0.0016 | -0.0247 | 0 | 0.4069 | -0.0266 | -0.0738 | 0.3983 | -0.1676 | 0.2896 | -55.3818 | -10.0677 | 19.943 | 9 | 0.1344 | 0.0211 | 0.0294 | 0.0262 | -0.0521 | 0.1062 | -0.0172 | -0.0576 | 0.0275 | 0.0165 | 0.0302 | -0.0079 | 0.1005 | -0.1889 | -0.008 | 0.0891 | -0.0083 | -0.0289 | 0.1032 | -0.0033 | 0.1184 | -57.1311 | -26.3241 | -2.1687 | 10 | 0.0047 | 0.0019 | 0.008 | 0.0007 | 0.0017 | 0.0006 | 0.0141 | -0.0823 | -0.046 | -0.0428 | 0.0275 | -0.0234 | -0.02 | -0.0863 | 0.0009 | 0.0935 | -0.0082 | -0.0123 | 0.0554 | 0.0151 | 0.0958 | -38.453 | -27.6484 | 7.7991 | 11 | 0.0074 | 0.0019 | 0.0007 | 0.0064 | -0.001 | 0.0018 | 0.0911 | 0.0252 | -0.05 | 0.0137 | 0.044 | -0.0309 | 0.0642 | 0.0745 | 0.0004 | 0.1229 | -0.0158 | -0.0276 | 0.0897 | -0.0163 | 0.1246 | -36.6957 | -32.9201 | 3.1067 | 12 | 0.002 | -0.0003 | 0.0013 | 0.0029 | 0.0027 | 0.0026 | 0.0013 | 0.0234 | 0.0014 | -0.0237 | 0.0346 | -0.0378 | 0.058 | 0.0229 | 0 | 0.1742 | 0.013 | -0.0334 | 0.1281 | -0.0329 | 0.134 | -40.7915 | -37.4648 | -5.8737 | 13 | 0.0323 | -0.0028 | -0.0002 | 0.0136 | 0.0218 | 0.0306 | -0.0206 | 0.108 | -0.0346 | -0.0019 | -0.0346 | -0.0432 | 0.0103 | -0.1314 | -0.0127 | 0.0643 | -0.0681 | -0.1364 | 0.1074 | -0.1827 | -0.0469 | -53.806 | -38.9061 | -16.4924 | 14 | -0.0027 | -0.0039 | -0.001 | 0.0008 | 0.0031 | -0.0044 | -0.0373 | 0.1483 | -0.0714 | 0.045 | 0.0638 | -0.0867 | -0.0149 | 0.0431 | 0 | 0.1554 | 0.0188 | -0.0107 | 0.1323 | -0.0328 | 0.2644 | -11.3742 | -47.365 | -35.7263 | 15 | 0.0391 | 0.0297 | 0.0251 | 0.0132 | 0.0064 | 0.0062 | 0.053 | 0.1316 | -0.0065 | -0.0523 | -0.0332 | -0.0072 | 0.1505 | 0.132 | 0.0004 | 0.1293 | 0.0183 | -0.0325 | 0.1015 | -0.0117 | 0.1011 | -25.9225 | -28.5975 | -38.0332 | 16 | 0.1883 | 0.076 | -0.0056 | 0.0629 | 0.0229 | 0.0149 | 0.0505 | -0.155 | 0.1848 | 0.0477 | -0.0148 | 0.0817 | 0.0513 | -0.0213 | 0.0378 | 0.1058 | -0.0285 | -0.0011 | 0.1304 | -0.0659 | 0.116 | -32.9061 | -19.324 | -17.4055 | 17 | 0.2716 | -0.0565 | 0.1531 | 0.1564 | -0.1116 | 0.1958 | 0.1009 | 0.0465 | 0.0425 | -0.1379 | -0.1764 | -0.1045 | 0.1025 | 0.1763 | -0.0596 | 0.0074 | -0.0598 | -0.0309 | 0.0877 | -0.001 | 0.0472 | -15.617 | -20.2669 | -28.0766 | 18 | -0.003 | -0.0007 | 0.0026 | 0.0027 | -0.009 | -0.0071 | -0.1061 | -0.0061 | -0.005 | -0.0104 | 0.0777 | 0.0094 | 0.1215 | 0.0901 | 0 | 0.1832 | -0.004 | 0.0082 | 0.1756 | 0.0163 | 0.1979 | -62.1143 | -47.1933 | 8.6958 | 19 | 0.0254 | -0.0308 | 0.0244 | 0.0221 | 0.0141 | 0.0137 | 0.0393 | -0.1903 | -0.0192 | 0.0872 | -0.0428 | 0.0303 | 0.1645 | -0.17 | -0.0076 | 0.1123 | -0.0389 | -0.0072 | 0.1347 | 0.0108 | 0.0919 | -53.7151 | -29.8873 | 11.6274 | 20 | 0.5262 | -0.0933 | -0.1361 | 0.0933 | 0.059 | 0.174 | 0.137 | 0.3104 | 0.362 | -0.0375 | -0.012 | -0.0943 | 0.0128 | -0.0497 | 0.1155 | 0.0591 | -0.0398 | -0.0302 | 0.0467 | 0.0526 | 0.1284 | -47.074 | -19.997 | -8.9629 | 21 | 0.1874 | -0.0066 | 0.1721 | 0.0941 | -0.0012 | 0.072 | -0.0243 | -0.046 | 0.0396 | 0.0304 | -0.0304 | 0.0452 | 0.0159 | -0.1754 | -0.0176 | 0.0714 | 0.0029 | -0.0063 | 0.1546 | -0.0227 | 0.1022 | -64.5444 | -22.1004 | 1.8637 |
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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 7 through 33 )A7 - 33 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 34 through 63 )A34 - 63 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 64 through 133 )A64 - 133 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 134 through 144 )A134 - 144 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 6 through 20 )B6 - 20 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 21 through 33 )B21 - 33 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 34 through 63 )B34 - 63 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 64 through 70 )B64 - 70 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 71 through 112 )B71 - 112 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 113 through 122 )B113 - 122 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 123 through 127 )B123 - 127 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 128 through 133 )B128 - 133 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 134 through 144 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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