Software | Name | Version | Classification |
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MOSFLM | | data reductionSCALA | 3.2.25data scalingMOLREP | | phasingPHENIX | | refinementPDB_EXTRACT | 3.15 | data extraction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.453 Å / FOM work R set: 0.8734 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1993 | 1679 | 5.01 % | Random selection |
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Rwork | 0.1798 | 31833 | - | - |
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obs | 0.1809 | 33512 | 97.69 % | - |
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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: 68.38 Å2 / Biso mean: 24.27 Å2 / Biso min: 9.13 Å2 |
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Refinement step | Cycle: final / Resolution: 1.75→46.453 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2691 | 0 | 23 | 373 | 3087 |
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Biso mean | - | - | 31.02 | 34.94 | - |
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Num. residues | - | - | - | - | 354 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 2767 | X-RAY DIFFRACTION | f_angle_d0.887 | 3753 | X-RAY DIFFRACTION | f_chiral_restr0.059 | 430 | X-RAY DIFFRACTION | f_plane_restr0.004 | 485 | X-RAY DIFFRACTION | f_dihedral_angle_d14 | 1050 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.75-1.8015 | 0.2934 | 138 | 0.2795 | 2573 | X-RAY DIFFRACTION | 97 | 1.8015-1.8597 | 0.2515 | 126 | 0.2373 | 2603 | X-RAY DIFFRACTION | 97 | 1.8597-1.9261 | 0.227 | 127 | 0.2104 | 2604 | X-RAY DIFFRACTION | 97 | 1.9261-2.0033 | 0.2349 | 123 | 0.2027 | 2591 | X-RAY DIFFRACTION | 96 | 2.0033-2.0944 | 0.2356 | 146 | 0.1956 | 2599 | X-RAY DIFFRACTION | 97 | 2.0944-2.2049 | 0.2277 | 127 | 0.186 | 2614 | X-RAY DIFFRACTION | 97 | 2.2049-2.343 | 0.1856 | 162 | 0.1806 | 2605 | X-RAY DIFFRACTION | 97 | 2.343-2.5239 | 0.194 | 121 | 0.1734 | 2678 | X-RAY DIFFRACTION | 98 | 2.5239-2.7779 | 0.1872 | 156 | 0.1857 | 2674 | X-RAY DIFFRACTION | 99 | 2.7779-3.1797 | 0.2254 | 151 | 0.1805 | 2721 | X-RAY DIFFRACTION | 99 | 3.1797-4.0058 | 0.1958 | 146 | 0.1573 | 2749 | X-RAY DIFFRACTION | 99 | 4.0058-46.47 | 0.1629 | 156 | 0.1594 | 2822 | X-RAY DIFFRACTION | 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 | 3.1597 | 0.2025 | -1.1208 | 5.436 | 2.4221 | 7.2352 | -0.2883 | -0.3294 | -0.69 | 0.6178 | 0.0801 | -0.194 | 1.6502 | 0.1536 | 0.1418 | 0.367 | 0.0063 | 0.0086 | 0.2627 | 0.0311 | 0.2958 | -3.3991 | -5.7378 | 20.808 | 2 | 3.8129 | -0.9813 | -1.2015 | 0.3067 | 0.191 | 0.5128 | -0.1968 | 0.0514 | 0.1178 | 0.1552 | 0.1068 | 0.0298 | 0.0097 | 0.009 | 0.0974 | 0.1338 | 0.0087 | 0.0079 | 0.1752 | 0.012 | 0.1649 | -11.0796 | 5.8603 | 28.8058 | 3 | 0.7107 | 0.282 | 0.5938 | 0.6223 | -0.2406 | 3.9542 | -0.0244 | 0.0162 | -0.1516 | -0.0691 | 0.0402 | -0.0793 | 0.2171 | 0.1591 | -0.0195 | 0.121 | -0.0105 | 0.0124 | 0.1138 | -0.0099 | 0.1094 | -0.5273 | 1.9378 | 10.3741 | 4 | 1.5329 | 0.1438 | 0.3237 | 1.5833 | -0.3218 | 2.3332 | 0.0303 | -0.0682 | 0.1219 | 0.0577 | -0.0152 | 0.0267 | -0.0786 | 0.118 | -0.0304 | 0.1148 | -0.0127 | -0.0059 | 0.1291 | -0.005 | 0.1566 | -0.6805 | 12.5643 | 10.1619 | 5 | 1.3115 | -0.8024 | -0.7338 | 1.9984 | 0.5588 | 0.5097 | -0.1629 | -0.1977 | 0.0744 | 0.2499 | 0.0339 | 0.1148 | -0.0916 | 0.0259 | 0.111 | 0.202 | 0.0159 | -0.0478 | 0.1634 | -0.0475 | 0.1803 | -3.0817 | 24.6398 | 12.7834 | 6 | 3.8027 | 1.9731 | -2.589 | 1.509 | -1.3218 | 3.0707 | 0.1467 | -0.3472 | 0.6649 | 0.1954 | 0.1524 | 0.8148 | -0.0061 | -0.2301 | -0.136 | 0.2795 | 0.0389 | -0.009 | 0.2419 | -0.055 | 0.429 | -14.762 | 25.9652 | 15.7364 | 7 | 0.255 | 0.0556 | 0.141 | 1.6526 | 0.7752 | 0.5463 | -0.0462 | -0.0461 | 0.1823 | -0.2874 | 0.0395 | 0.3251 | -0.2922 | -0.0184 | 0.0021 | 0.1659 | 0.0147 | -0.0495 | 0.1515 | -0.0019 | 0.1795 | -7.0781 | 17.514 | 6.7679 | 8 | 0.5721 | -0.0411 | -0.3718 | 2.0385 | -0.2005 | 1.5608 | -0.1286 | -0.0148 | 0.1458 | -0.19 | 0.0261 | 0.5148 | -0.2276 | -0.1179 | 0.0478 | 0.1843 | 0.0247 | -0.0907 | 0.1836 | -0.0161 | 0.2677 | -11.5171 | 18.1193 | 5.2586 | 9 | 0.5803 | -0.2142 | 0.6817 | 1.2563 | -0.6572 | 1.4392 | -0.0651 | 0.6919 | 0.4317 | -0.2108 | 0.0167 | 0.1312 | 0.0882 | -0.1652 | -0.0425 | 0.1256 | 0.0111 | -0.0006 | 0.3046 | 0.055 | 0.1961 | -19.3177 | 7.5613 | 13.8195 | 10 | 0.8521 | -0.3509 | -0.5428 | 1.4748 | 1.1842 | 2.2576 | -0.4301 | 0.5379 | 0.3926 | -0.1983 | 0.3177 | 0.4286 | 0.1264 | -0.4471 | -0.2613 | 0.1041 | -0.041 | -0.0491 | 0.3024 | 0.1099 | 0.2151 | -14.8367 | 4.2116 | 12.0786 | 11 | 9.26 | 0.4792 | -0.5826 | 5.7177 | 1.8091 | 8.2715 | -0.0761 | 0.4411 | 0.369 | -0.0455 | -0.2776 | -0.7329 | 0.5206 | 0.4815 | 0.3369 | 0.2219 | 0.0383 | -0.0213 | 0.2395 | 0.0298 | 0.2327 | 19.4503 | 22.345 | 10.505 | 12 | 0.4161 | -0.997 | -0.4687 | 2.6952 | 0.7455 | 1.3133 | -0.0623 | -0.1406 | 0.5031 | -0.1524 | -0.0706 | -0.2348 | -0.3717 | -0.0236 | 0.1644 | 0.2308 | 0.0147 | -0.0766 | 0.2005 | -0.07 | 0.3422 | 5.8592 | 31.2875 | 13.7318 | 13 | 1.74 | -0.6074 | 1.6965 | 0.7043 | -1.2998 | 2.593 | -0.0438 | 0.0537 | 0.0033 | -0.026 | 0.0093 | -0.0301 | 0.0996 | 0.0869 | -0.0034 | 0.1406 | 0.0186 | 0.0251 | 0.1599 | -0.0098 | 0.1765 | 16.703 | 14.3361 | 17.6539 | 14 | 1.9294 | -0.2023 | 0.0277 | 1.4901 | -0.867 | 2.3286 | -0.0336 | 0.0249 | 0.0855 | -0.009 | 0.1141 | -0.0186 | 0.0451 | -0.2294 | -0.102 | 0.178 | -0.0346 | -0.0136 | 0.1996 | -0.0221 | 0.1656 | 8.1139 | 12.3388 | 23.988 | 15 | 2.3946 | -0.8255 | -0.9146 | 1.0024 | 0.9007 | 1.4234 | 0.0706 | 0.1198 | 0.0698 | -0.0846 | -0.157 | 0.0262 | -0.3302 | -0.1691 | 0.0849 | 0.2293 | -0.0036 | -0.0233 | 0.2005 | -0.0039 | 0.1447 | -2.7247 | 13.3893 | 30.2926 | 16 | 1.1893 | -0.0958 | -0.4084 | 3.6538 | 0.743 | 0.5542 | -0.0236 | 0.1146 | 0.2327 | -0.2331 | 0.0554 | 0.0005 | -0.4964 | -0.1581 | 0.0442 | 0.3669 | 0.0236 | -0.0614 | 0.1561 | 0.0049 | 0.1783 | -3.0973 | 20.8347 | 37.1424 | 17 | 1.728 | 0.6037 | -0.4361 | 0.3425 | 0.2536 | 1.1934 | 0.0141 | -0.221 | -0.0392 | 0.0707 | 0.0083 | 0.1832 | 0.0459 | 0.0937 | -0.0217 | 0.172 | 0.033 | 0.0165 | 0.1571 | 0.0026 | 0.1506 | 7.4894 | 14.6379 | 32.2378 | 18 | 1.6662 | 0.5089 | -0.26 | 4.2898 | -2.0331 | 1.8846 | -0.1399 | -0.0309 | 0.0176 | 0.35 | 0.0352 | -0.119 | -0.1921 | -0.0543 | 0.0932 | 0.2061 | 0.0453 | 0.0592 | 0.2032 | -0.0043 | 0.1783 | 5.4874 | 19.1373 | 37.2884 | 19 | 1.0762 | -0.2103 | -0.0296 | 1.6659 | -0.5243 | 0.9358 | 0.1018 | -0.2114 | 0.2246 | 0.4163 | -0.0223 | -0.0067 | -0.4233 | 0.1807 | -0.076 | 0.2448 | -0.0161 | 0.0083 | 0.162 | -0.031 | 0.1646 | 13.8122 | 24.0738 | 30.9783 | 20 | 1.7675 | -0.04 | 0.1399 | 2.1305 | 0.1084 | 2.906 | 0.1452 | 0.0489 | 0.2634 | 0.1685 | -0.2025 | -0.1984 | -0.7226 | 0.462 | 0.0479 | 0.23 | -0.0245 | -0.0052 | 0.1746 | -0.0147 | 0.2352 | 16.9219 | 26.2131 | 25.6288 |
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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 2 through 12 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 13 through 35 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 36 through 54 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 55 through 79 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 80 through 95 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 96 through 113 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 114 through 133 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 134 through 155 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 156 through 168 )A0 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 169 through 180 )A0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 2 through 10 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 11 through 35 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 36 through 54 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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