Software | Name | Version | Classification | NB |
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PHENIX | | refinement | XDS | | data reduction | XSCALE | | data scaling | PHASER | 2.5.6phasing | PDB_EXTRACT | 3.24 | data extraction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tro Resolution: 2.128→44.748 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.84
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2292 | 1308 | 5 % |
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Rwork | 0.1718 | - | - |
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obs | 0.1747 | 26149 | 99.54 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 112.96 Å2 / Biso mean: 36.0904 Å2 / Biso min: 15.17 Å2 |
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Refinement step | Cycle: final / Resolution: 2.128→44.748 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3284 | 0 | 56 | 324 | 3664 |
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Biso mean | - | - | 30.3 | 37.59 | - |
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Num. residues | - | - | - | - | 408 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 3416 | X-RAY DIFFRACTION | f_angle_d0.428 | 4616 | X-RAY DIFFRACTION | f_chiral_restr0.031 | 514 | X-RAY DIFFRACTION | f_plane_restr0.003 | 600 | X-RAY DIFFRACTION | f_dihedral_angle_d7.456 | 2512 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.1281-2.2133 | 0.3229 | 140 | 0.2541 | 2663 | 2803 | 96 | 2.2133-2.314 | 0.2706 | 144 | 0.1989 | 2741 | 2885 | 100 | 2.314-2.436 | 0.2565 | 145 | 0.1887 | 2757 | 2902 | 100 | 2.436-2.5886 | 0.2446 | 146 | 0.1806 | 2757 | 2903 | 100 | 2.5886-2.7884 | 0.2779 | 144 | 0.1802 | 2754 | 2898 | 100 | 2.7884-3.069 | 0.2427 | 147 | 0.1858 | 2781 | 2928 | 100 | 3.069-3.5129 | 0.2239 | 146 | 0.1616 | 2771 | 2917 | 100 | 3.5129-4.4253 | 0.1989 | 146 | 0.1463 | 2779 | 2925 | 100 | 4.4253-44.7579 | 0.1912 | 150 | 0.1598 | 2838 | 2988 | 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 | 4.6041 | 5.8699 | 1.4245 | 7.6097 | 1.7362 | 1.8529 | 0.0254 | -0.5492 | -0.2275 | -0.2488 | -0.402 | -0.16 | 0.0492 | 0.0877 | 0.3007 | 0.2066 | 0.0588 | 0.0046 | 0.2429 | 0.0709 | 0.2644 | 135.4163 | 101.1269 | 27.302 | 2 | 2.1927 | 1.0803 | -1.7129 | 2.8682 | -3.3247 | 6.1112 | -0.1254 | 0.2001 | 0.0306 | -0.0275 | 0.0599 | -0.0195 | 0.1347 | -0.5401 | 0.0479 | 0.1804 | -0.0334 | -0.007 | 0.1604 | -0.0152 | 0.2606 | 120.5781 | 102.5469 | 17.6916 | 3 | 7.7023 | -2.321 | -3.1764 | 7.1236 | 2.1339 | 7.5801 | -0.209 | 1.2056 | 0.3128 | -1.6951 | 0.077 | 1.1855 | -0.7526 | -0.5923 | 0.1716 | 0.5539 | -0.0544 | -0.1169 | 0.5483 | 0.0474 | 0.4905 | 118.1382 | 111.7299 | 0.8022 | 4 | 5.9993 | -5.3609 | -1.5216 | 9.6239 | 2.5798 | 4.7097 | -0.0801 | -0.0384 | -0.4789 | 0.1122 | -0.1811 | 0.0404 | 0.1201 | -0.0715 | 0.2007 | 0.1738 | -0.0524 | 0.0548 | 0.2017 | -0.0239 | 0.2354 | 129.2188 | 111.8865 | 6.5068 | 5 | 4.9188 | -1.3628 | -0.8956 | 7.032 | 2.5152 | 6.2025 | -0.6072 | 0.7138 | -0.7014 | -1.0084 | 0.5232 | -0.4992 | 0.9732 | 0.1762 | -0.0093 | 0.5164 | -0.049 | 0.1173 | 0.2317 | -0.0312 | 0.3258 | 129.831 | 95.3981 | 4.9357 | 6 | 7.2204 | -1.2552 | 1.3245 | 0.4037 | 0.4616 | 2.3837 | -0.0163 | 0.0726 | 0.0698 | -0.097 | -0.1821 | -0.0057 | 0.0778 | -0.2416 | 0.1613 | 0.2409 | -0.0496 | 0.0178 | 0.1757 | -0.0466 | 0.2286 | 115.4746 | 100.2701 | 15.8596 | 7 | 1.6361 | 0.7825 | -1.7927 | 1.9839 | 2.3305 | 8.1205 | 0.149 | -0.1413 | -0.0989 | -0.0282 | 0.0069 | -0.1638 | -0.0134 | 0.2512 | -0.1724 | 0.1378 | 0.0531 | -0.011 | 0.1852 | 0.028 | 0.2774 | 130.8588 | 104.1182 | 25.4616 | 8 | 2.0219 | 2.8755 | -2.7604 | 5.2957 | -5.429 | 6.2316 | -0.213 | -1.1042 | 0.5954 | 1.8364 | 0.289 | -0.936 | -0.9587 | 0.0488 | -0.0089 | 0.5529 | 0.0646 | -0.0759 | 0.5634 | -0.0977 | 0.5519 | 130.374 | 113.7335 | 42.193 | 9 | 6.3406 | 0.5732 | -0.5331 | 4.8936 | 0.0677 | 2.6246 | -0.0323 | -0.4595 | -0.5085 | 0.2336 | -0.01 | 0.147 | 0.3609 | -0.1348 | 0.0649 | 0.2418 | -0.0117 | 0.0374 | 0.3011 | 0.0367 | 0.176 | 121.769 | 101.3872 | 37.5507 | 10 | 8.2249 | 3.9995 | 2.5272 | 5.6886 | 4.2844 | 4.1077 | 0.0133 | -1.0691 | 0.9013 | 1.7518 | 0.4002 | -0.0308 | 0.5778 | -0.7598 | -0.341 | 0.4005 | 0.0817 | -0.0842 | 0.5717 | -0.1767 | 0.3884 | 81.3306 | 101.5839 | 9.4387 | 11 | 5.5193 | -4.8709 | -0.52 | 6.0114 | 0.8593 | 2.0271 | -0.0864 | -0.0863 | 0.1307 | -0.1363 | 0.0255 | 0.087 | -0.2773 | 0.0798 | 0.0182 | 0.2441 | -0.056 | -0.0424 | 0.2192 | -0.0095 | 0.2349 | 100.7283 | 98.4965 | 8.0019 | 12 | 2.7976 | 0.6379 | 1.6488 | 1.8849 | -1.7226 | 5.4419 | 0.0063 | 0.0104 | -0.108 | -0.132 | 0.105 | -0.0794 | 0.2775 | -0.0477 | -0.1469 | 0.1878 | 0.0232 | 0.0169 | 0.169 | -0.0351 | 0.2696 | 101.8056 | 83.8652 | -2.3641 | 13 | 6.656 | 3.1445 | -2.0662 | 2.3882 | -1.1117 | 8.0873 | -0.2518 | 1.0292 | -0.6188 | -0.2938 | 0.453 | 0.1958 | -0.0253 | -0.1837 | 0.025 | 0.5156 | -0.1084 | -0.0544 | 0.39 | -0.0999 | 0.5035 | 94.7175 | 78.216 | -18.8097 | 14 | 5.6201 | 4.6009 | -1.5712 | 7.2052 | -1.7259 | 2.3042 | -0.1644 | -0.0647 | -0.2726 | 0.2472 | -0.0367 | -0.0232 | 0.2617 | -0.1448 | 0.1707 | 0.2451 | 0.0217 | -0.0043 | 0.2317 | 0.009 | 0.2696 | 91.3364 | 90.5733 | -13.5638 | 15 | 2.7434 | -2.3287 | -0.2954 | 3.5051 | -2.4835 | 5.9805 | 0.1687 | 0.9314 | 0.6955 | -0.4525 | -0.3624 | -0.7406 | -0.424 | 0.8348 | 0.0953 | 0.333 | -0.121 | 0.0088 | 0.4104 | 0.0538 | 0.3514 | 106.8683 | 95.4217 | -14.2729 | 16 | 1.263 | 1.7679 | -0.3755 | 8.8837 | 1.068 | 1.3546 | -0.015 | 0.0212 | -0.2315 | -0.1584 | -0.0347 | -0.5579 | 0.0143 | 0.1009 | 0.064 | 0.2289 | -0.0006 | 0.0122 | 0.2584 | 0.0126 | 0.2225 | 105.6682 | 79.8181 | -3.6626 | 17 | 1.2889 | 0.0323 | -0.4196 | 1.8583 | -3.2579 | 6.6879 | -0.0584 | -0.0475 | 0.1657 | 0.1092 | 0.0567 | 0.0226 | -0.4868 | -0.1987 | -0.0448 | 0.1988 | -0.0073 | -0.0127 | 0.1191 | -0.0103 | 0.197 | 98.0814 | 93.6913 | 5.7505 | 18 | 6.0159 | 1.8204 | 2.0442 | 6.773 | -1.33 | 3.4653 | 0.4086 | -1.0754 | 0.1477 | 1.2504 | -0.359 | 0.9297 | -0.0343 | -1.4909 | 0.0958 | 0.4962 | -0.0339 | 0.1394 | 0.4815 | -0.086 | 0.4047 | 88.1108 | 91.1023 | 22.1529 | 19 | 7.1182 | 3.0701 | -1.8996 | 5.5143 | 0.0454 | 3.9783 | 0.0736 | -0.1027 | 0.0945 | 0.3542 | -0.0623 | -0.2185 | -0.0757 | 0.3849 | -0.0001 | 0.2385 | 0.0066 | -0.0224 | 0.2246 | 0.0198 | 0.1707 | 102.6148 | 85.8729 | 18.1945 | 20 | 7.0043 | 2.1521 | 4.7436 | 4.9226 | 3.0826 | 6.4421 | -0.0867 | -0.9301 | -0.4771 | 1.5804 | 0.6104 | -0.1018 | -1.0259 | -0.9342 | -0.4276 | 0.5812 | -0.0368 | 0.0115 | 0.4544 | 0.1812 | 0.3635 | 142.5423 | 118.6764 | 29.2248 |
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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 'B' and (resid 9 through 31 )B9 - 31 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 32 through 63 )B32 - 63 | 3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resid 64 through 78 )B64 - 78 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 79 through 91 )B79 - 91 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 92 through 106 )B92 - 106 | 6 | X-RAY DIFFRACTION | 6 | chain 'C' and (resid 5 through 31 )C5 - 31 | 7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 32 through 63 )C32 - 63 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 64 through 78 )C64 - 78 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 79 through 105 )C79 - 105 | 10 | X-RAY DIFFRACTION | 10 | chain 'R' and (resid 4 through 8 )R4 - 8 | 11 | X-RAY DIFFRACTION | 11 | chain 'R' and (resid 9 through 32 )R9 - 32 | 12 | X-RAY DIFFRACTION | 12 | chain 'R' and (resid 33 through 63 )R33 - 63 | 13 | X-RAY DIFFRACTION | 13 | chain 'R' and (resid 64 through 78 )R | | | | | | | | | | | | | | | | | | | | | | | | | |
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