Software | Name | Version | Classification |
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XDS | | data reductionXSCALE | | data scalingPHENIX | 1.19rc4-4035 | refinementPDB_EXTRACT | 3.27 | data extractionMoRDa | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vpe Resolution: 1.6→44.9 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.34 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1935 | 2069 | 0.96 % |
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Rwork | 0.164 | 214502 | - |
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obs | 0.1643 | 216571 | 99.69 % |
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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: 84.31 Å2 / Biso mean: 28.3993 Å2 / Biso min: 11.25 Å2 |
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Refinement step | Cycle: final / Resolution: 1.6→44.9 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 11833 | 0 | 64 | 1933 | 13830 |
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Biso mean | - | - | 37.13 | 36.85 | - |
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Num. residues | - | - | - | - | 1644 |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6-1.64 | 0.3334 | 146 | 0.2779 | 14266 | 14412 | 100 | 1.64-1.68 | 0.2501 | 131 | 0.2465 | 14271 | 14402 | 100 | 1.68-1.72 | 0.2626 | 150 | 0.22 | 14230 | 14380 | 100 | 1.72-1.77 | 0.2437 | 103 | 0.1976 | 14331 | 14434 | 100 | 1.77-1.83 | 0.2261 | 134 | 0.1943 | 14236 | 14370 | 100 | 1.83-1.9 | 0.2183 | 162 | 0.1876 | 14262 | 14424 | 100 | 1.9-1.97 | 0.2341 | 119 | 0.1919 | 14277 | 14396 | 100 | 1.97-2.06 | 0.1843 | 128 | 0.1683 | 14329 | 14457 | 100 | 2.06-2.17 | 0.1974 | 153 | 0.1658 | 14215 | 14368 | 99 | 2.17-2.31 | 0.2099 | 134 | 0.1634 | 14301 | 14435 | 100 | 2.31-2.49 | 0.1901 | 151 | 0.1639 | 14260 | 14411 | 100 | 2.49-2.74 | 0.2108 | 149 | 0.1688 | 14299 | 14448 | 100 | 2.74-3.13 | 0.1848 | 137 | 0.1621 | 14351 | 14488 | 100 | 3.13-3.95 | 0.1696 | 140 | 0.1445 | 14371 | 14511 | 100 | 3.95-44.9 | 0.1632 | 132 | 0.1412 | 14503 | 14635 | 99 |
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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 | 1.2476 | 0.0386 | 0.3376 | 1.1895 | 0.027 | 1.493 | 0.0189 | 0.0775 | -0.0671 | -0.0601 | 0.0237 | -0.1164 | 0.1412 | 0.1123 | -0.0342 | 0.116 | 0.0208 | 0.0296 | 0.1155 | -0.0152 | 0.1183 | 39.6215 | -10.8449 | 11.6692 | 2 | 2.2067 | -0.1026 | 1.5968 | 1.5281 | 0.4095 | 2.5902 | -0.2986 | -0.1146 | 0.2818 | 0.0312 | -0.0245 | 0.0817 | -0.3498 | -0.1235 | 0.2574 | 0.2409 | 0.0093 | -0.0562 | 0.0972 | 0.0246 | 0.1997 | 20.4941 | 18.835 | 2.6394 | 3 | 1.4799 | -1.1769 | 2.7225 | 1.9647 | -2.563 | 7.3658 | 0.063 | 0.1676 | 0.0523 | -0.1273 | 0.046 | 0.0219 | 0.1962 | 0.0662 | -0.1497 | 0.1052 | -0.0383 | -0.0085 | 0.1259 | 0.0083 | 0.1529 | 37.334 | 5.2149 | 10.7735 | 4 | 2.0681 | -0.0113 | -0.1863 | 1.9332 | -0.5871 | 1.3042 | 0.0518 | -0.0154 | 0.1964 | 0.1488 | -0.014 | 0.041 | -0.0551 | -0.0254 | -0.0453 | 0.1294 | -0.0186 | 0.0264 | 0.079 | -0.004 | 0.1224 | 4.8423 | -4.7062 | 5.9658 | 5 | 1.177 | -0.0317 | 0.0704 | 1.3847 | -0.5615 | 1.5101 | 0.0453 | 0.0699 | -0.0174 | -0.0335 | 0.0179 | 0.0999 | 0.1592 | -0.0464 | -0.0523 | 0.1397 | -0.0326 | 0.0013 | 0.1216 | 0.0034 | 0.1244 | 1.9205 | -14.7117 | 0.8711 | 6 | 2.3338 | -1.6526 | -1.2444 | 2.6353 | 0.7643 | 1.4518 | -0.0179 | -0.2482 | 0.4279 | 0.2675 | 0.2096 | -0.5605 | -0.1108 | 0.2803 | -0.1551 | 0.2405 | 0.011 | -0.0606 | 0.233 | -0.0515 | 0.238 | 30.5901 | -12.9475 | -22.1828 | 7 | 1.3683 | -0.4092 | -1.1463 | 1.7912 | -0.4054 | 1.378 | -0.0988 | -0.0326 | -0.0205 | -0.109 | 0.0213 | -0.1705 | 0.0862 | 0.1101 | 0.0452 | 0.2751 | -0.0007 | -0.0457 | 0.2124 | -0.011 | 0.1323 | 9.4735 | -13.1568 | -11.6433 | 8 | 2.9963 | -0.6157 | -0.0712 | 2.2257 | 0.3389 | 1.9626 | -0.072 | 0.2477 | -0.1612 | -0.0764 | -0.0021 | 0.1828 | 0.0298 | -0.3147 | 0.0308 | 0.0844 | -0.0182 | -0.0013 | 0.1973 | 0.0172 | 0.1101 | 17.7478 | -47.2146 | 53.4128 | 9 | 1.0985 | 0.0597 | 0.0033 | 1.1747 | 0.2561 | 2.0647 | 0.0099 | 0.0546 | 0.095 | -0.0116 | -0.0242 | 0.0385 | -0.1846 | -0.1924 | 0.0062 | 0.0888 | 0.0182 | -0.0041 | 0.1505 | 0.0224 | 0.115 | 17.2697 | -39.4407 | 57.7964 | 10 | 1.6599 | -0.5737 | 0.5315 | 2.0166 | -0.4178 | 1.3557 | -0.0193 | -0.131 | -0.1544 | 0.1578 | 0.0567 | 0.1714 | -0.0086 | 0.1147 | -0.0196 | 0.1536 | -0.0137 | 0.0217 | 0.1685 | 0.0356 | 0.1116 | 1.9353 | -36.3476 | 24.255 | 11 | 3.5747 | 2.2895 | 3.8407 | 2.8874 | 2.7693 | 4.1259 | -0.1459 | -0.0055 | 0.0276 | -0.3051 | -0.0021 | 0.0734 | -0.304 | -0.0487 | 0.1666 | 0.1804 | 0.0011 | 0.0446 | 0.2642 | 0.0863 | 0.1727 | 18.4087 | -38.2089 | 40.4824 | 12 | 5.7062 | 0.7868 | 0.8953 | 2.0568 | 0.3301 | 2.3443 | -0.1394 | -0.0343 | 0.1888 | 0.0057 | 0.0264 | -0.2342 | -0.031 | 0.2605 | 0.0781 | 0.1417 | 0.0334 | -0.0071 | 0.2111 | 0.0027 | 0.2643 | -18.6227 | -42.6353 | 49.3896 | 13 | 2.2564 | -0.0017 | 0.0479 | 2.4755 | 0.2484 | 1.1526 | -0.1341 | -0.2447 | 0.0142 | 0.2345 | 0.1331 | -0.1255 | 0.0475 | 0.0664 | -0.0074 | 0.1475 | 0.0332 | -0.0008 | 0.2748 | -0.014 | 0.2355 | -22.8695 | -45.1809 | 58.1109 | 14 | 6.1961 | -0.1258 | 0.4755 | 7.4391 | 1.4387 | 4.301 | -0.2451 | -0.5029 | -0.048 | 0.3159 | 0.0823 | 0.3098 | -0.0576 | -0.1647 | 0.1499 | 0.1903 | 0.0216 | 0.0198 | 0.2675 | 0.0502 | 0.2378 | -4.5762 | -70.8692 | 54.424 | 15 | 2.9895 | 0.4157 | 0.4962 | 1.1416 | 0.1793 | 1.2664 | -0.0514 | -0.0598 | -0.0037 | 0.0114 | 0.0202 | -0.1198 | -0.0602 | 0.0237 | 0.0335 | 0.1756 | -0.0091 | -0.0027 | 0.1893 | -0.0114 | 0.2111 | 6.0346 | -69.2318 | 48.4243 | 16 | 6.5385 | -3.5729 | 0.3558 | 9.2906 | -0.2587 | 8.063 | -0.3776 | -0.6199 | -0.5924 | 0.4918 | 0.5036 | -0.4586 | 0.2851 | 0.5983 | -0.0816 | 0.2624 | 0.0354 | -0.0178 | 0.2765 | -0.0009 | 0.2972 | -18.5575 | -60.1028 | 60.4052 |
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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 0 through 196 )A0 - 196 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 197 through 373 )A197 - 373 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 374 through 411 )A374 - 411 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 1 through 112 )B1 - 112 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 113 through 195 )B113 - 195 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 196 through 373 )B196 - 373 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 374 through 411 )B374 - 411 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 0 through 56 )C0 - 56 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 57 through 196 )C57 - 196 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 197 through 373 )C197 - 373 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 374 through 411 )C374 - 411 | 12 | X-RAY DIFFRACTION | 12 | chain 'D' and (resid 2 through 91 )D2 - 91 | 13 | X-RAY DIFFRACTION | 13 | chain 'D' and (resid 92 through 196 )D | | | | | | | | | | | | | | | | | | | | | | | | | |
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