Software | Name | Classification |
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XDS | data reductionXSCALE | data scalingMoRDa | phasingXDS | data reduction Coot | model buildingPHENIX | refinementPDB_EXTRACT | data extraction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ibo Resolution: 1.65→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.83
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1639 | 1965 | 1.68 % |
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Rwork | 0.1355 | - | - |
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obs | 0.136 | 116823 | 99.32 % |
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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: 70.25 Å2 / Biso mean: 14.9941 Å2 / Biso min: 4.72 Å2 |
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Refinement step | Cycle: final / Resolution: 1.65→50 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7763 | 0 | 312 | 1160 | 9235 |
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Biso mean | - | - | 15.2 | 27.75 | - |
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Num. residues | - | - | - | - | 1031 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 8355 | X-RAY DIFFRACTION | f_angle_d0.971 | 11372 | X-RAY DIFFRACTION | f_chiral_restr0.065 | 1262 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1588 | X-RAY DIFFRACTION | f_dihedral_angle_d13.05 | 5001 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.65-1.6913 | 0.2345 | 122 | 0.2328 | 7562 | 7684 | 92 | 1.6913-1.737 | 0.2317 | 159 | 0.1944 | 8083 | 8242 | 99 | 1.737-1.7881 | 0.2318 | 162 | 0.1764 | 8155 | 8317 | 100 | 1.7881-1.8458 | 0.1818 | 150 | 0.1527 | 8150 | 8300 | 100 | 1.8458-1.9118 | 0.1875 | 159 | 0.1443 | 8174 | 8333 | 100 | 1.9118-1.9883 | 0.1924 | 114 | 0.1526 | 8213 | 8327 | 100 | 1.9883-2.0788 | 0.1625 | 119 | 0.1307 | 8232 | 8351 | 100 | 2.0788-2.1884 | 0.161 | 151 | 0.1248 | 8212 | 8363 | 100 | 2.1884-2.3255 | 0.1398 | 131 | 0.1234 | 8216 | 8347 | 100 | 2.3255-2.5051 | 0.1644 | 143 | 0.1271 | 8268 | 8411 | 100 | 2.5051-2.7571 | 0.1428 | 157 | 0.1272 | 8271 | 8428 | 100 | 2.7571-3.1559 | 0.1528 | 120 | 0.1266 | 8312 | 8432 | 100 | 3.1559-3.9756 | 0.1414 | 155 | 0.1199 | 8382 | 8537 | 100 | 3.9756-41.1232 | 0.1568 | 123 | 0.1289 | 8628 | 8751 | 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 | 2.1213 | 1.8771 | -0.1991 | 3.3154 | -1.0304 | 0.7877 | -0.3434 | 0.138 | 0.7787 | -0.3162 | -0.0575 | 0.0292 | -0.5691 | 0.1948 | 0.1405 | 0.204 | -0.0187 | -0.057 | 0.1469 | 0.0329 | 0.2705 | -40.5006 | 15.9568 | 9.9179 | 2 | 1.6283 | 0.1416 | 0.5868 | 3.7958 | -0.6618 | 2.2156 | -0.0016 | -0.2281 | 0.0705 | 0.1359 | 0.0015 | 0.1486 | -0.0366 | -0.0534 | 0.0606 | 0.0418 | -0.0014 | 0.0133 | 0.0888 | -0.0122 | 0.0964 | -46.1249 | 0.5877 | 19.0807 | 3 | 2.4736 | -0.8128 | -0.466 | 1.6564 | -0.1241 | 0.9821 | 0.0149 | -0.17 | -0.0999 | 0.0741 | -0.0118 | 0.285 | -0.0125 | -0.1052 | 0.0019 | 0.0668 | -0.0031 | -0.0059 | 0.1133 | -0.0016 | 0.0978 | -53.8828 | -2.5036 | 18.043 | 4 | 0.9353 | -0.4086 | 0.4899 | 0.9627 | -0.5407 | 1.1209 | 0.043 | -0.0571 | -0.1263 | -0.0741 | 0.0314 | 0.2295 | 0.0848 | -0.1278 | -0.0756 | 0.0626 | -0.0179 | -0.0106 | 0.0824 | -0.0004 | 0.1081 | -44.1724 | -11.7299 | 13.7446 | 5 | 1.4589 | -1.1981 | 1.5046 | 1.86 | -1.6907 | 2.9054 | 0.0897 | 0.0052 | -0.1612 | -0.1044 | -0.0113 | 0.1978 | 0.1645 | 0.0119 | -0.1029 | 0.0713 | -0.0039 | -0.0024 | 0.0667 | -0.0109 | 0.1047 | -40.2648 | -14.3798 | 10.8625 | 6 | 0.6513 | -0.1853 | 0.2847 | 0.7467 | -0.0845 | 0.4291 | -0.0238 | -0.1076 | 0.0044 | 0.0699 | 0.0122 | 0.0214 | -0.016 | -0.0172 | 0.0118 | 0.0579 | -0.0052 | 0.0054 | 0.0734 | -0.0041 | 0.0543 | -31.0676 | -3.3954 | 20.4472 | 7 | 2.0623 | 0.2723 | 1.2577 | 0.3867 | 0.6494 | 1.4538 | 0.1072 | -0.1036 | -0.3092 | 0.0883 | -0.2354 | -0.8205 | -0.0596 | 0.6415 | 0.0634 | 0.1978 | 0.0139 | -0.0507 | 0.3023 | 0.0629 | 0.3772 | 6.392 | -29.2082 | 20.6105 | 8 | 2.9572 | -0.6079 | 1.0772 | 1.2522 | -0.4229 | 2.0867 | 0.1135 | 0.1703 | -0.1368 | -0.1847 | -0.0692 | -0.0414 | 0.1617 | 0.097 | -0.0388 | 0.1044 | 0.016 | -0.0011 | 0.0537 | -0.0076 | 0.1034 | -12.7493 | -34.1033 | 8.7272 | 9 | 4.7986 | -1.5438 | 0.533 | 0.8482 | -0.0468 | 1.126 | 0.008 | 0.2222 | -0.286 | -0.1337 | -0.0838 | 0.2854 | 0.1698 | -0.0073 | 0.0498 | 0.1378 | -0.0029 | -0.0115 | 0.053 | 0.0073 | 0.1257 | -15.6381 | -42.8153 | 7.8513 | 10 | 5.2531 | -2.3006 | -0.449 | 1.4341 | 0.1858 | 0.7769 | -0.1011 | -0.0539 | -0.2828 | -0.0166 | 0.047 | 0.1849 | 0.095 | 0.0017 | 0.069 | 0.111 | -0.0093 | -0.0049 | 0.0764 | 0.0091 | 0.1269 | -18.9737 | -40.1406 | 11.8536 | 11 | 1.2061 | -0.5946 | 0.596 | 1.443 | -0.4903 | 1.1559 | 0.0268 | -0.0432 | -0.1718 | -0.0675 | -0.0088 | 0.0789 | 0.1346 | -0.0292 | -0.0605 | 0.0841 | -0.008 | 0 | 0.0528 | -0.0127 | 0.0904 | -25.6205 | -31.1926 | 12.5899 | 12 | 0.9018 | -0.5182 | 0.4841 | 1.0986 | -0.5553 | 1.3509 | -0.0049 | -0.0454 | -0.0508 | -0.0016 | 0.0055 | 0.0353 | 0.0309 | -0.0046 | -0.001 | 0.0587 | -0.0001 | 0.0114 | 0.0474 | -0.006 | 0.0645 | -23.9505 | -22.585 | 15.8751 | 13 | 1.3308 | -0.0441 | 0.3707 | 1.0473 | -0.0246 | 1.5371 | 0.1785 | 0.3251 | -0.1455 | -0.3246 | 0.0315 | 0.1194 | 0.3824 | 0.1148 | -0.1436 | 0.1688 | 0.0224 | -0.0391 | 0.1102 | -0.0331 | 0.1183 | -16.3845 | -22.0044 | 2.5718 | 14 | 3.9349 | 0.8827 | 1.4072 | 2.7051 | 1.7407 | 2.4441 | -0.1592 | 0.438 | 0.1115 | -0.5472 | 0.0224 | 0.1717 | -0.1389 | 0.1475 | 0.1223 | 0.1764 | 0.0059 | -0.0036 | 0.1577 | -0.0126 | 0.0887 | -12.55 | -13.1965 | -6.2625 | 15 | 0.4048 | -0.1867 | 0.1056 | 0.4611 | -0.604 | 1.2177 | -0.0093 | 0.0199 | -0.0351 | -0.0047 | -0.0117 | -0.0512 | 0.0512 | 0.0225 | 0.0162 | 0.0815 | -0.0014 | -0.0062 | 0.0934 | -0.014 | 0.1056 | -9.0844 | -18.8132 | 12.3943 | 16 | 2.028 | 1.157 | 0.2815 | 2.953 | 0.736 | 1.3735 | -0.069 | 0.1409 | -0.3523 | -0.1407 | 0.0806 | -0.1253 | 0.1612 | 0.0701 | 0.0196 | 0.076 | 0.0256 | 0.0147 | 0.0937 | -0.0151 | 0.1328 | 8.6517 | -18.9608 | 13.2462 | 17 | 1.9696 | 1.1351 | 0.1556 | 3.021 | 0.7202 | 1.1639 | 0.0103 | -0.1178 | -0.1256 | 0.0825 | -0.0266 | -0.1159 | 0.0702 | 0.0327 | 0.0131 | 0.0488 | 0.0072 | -0.0001 | 0.0848 | 0.0075 | 0.0773 | 12.0006 | -12.0459 | 20.9205 | 18 | 1.4218 | -1.1479 | 0.5406 | 4.6792 | -1.2372 | 0.9324 | 0.0139 | -0.0559 | -0.0016 | -0.0351 | -0.0669 | -0.1042 | 0.0533 | 0.0841 | 0.0608 | 0.0609 | -0.0057 | 0.0135 | 0.1079 | 0.0182 | 0.0772 | 19.6606 | -9.0421 | 21.3651 | 19 | 1.6222 | -0.5768 | -0.6209 | 0.8636 | 0.4766 | 1.1347 | 0.0052 | -0.0232 | 0.0741 | -0.0069 | 0.0088 | -0.0948 | -0.0491 | 0.1239 | -0.0318 | 0.0548 | -0.0094 | -0.0126 | 0.0741 | 0.003 | 0.0618 | 8.5504 | 0.7616 | 17.1585 | 20 | 1.6832 | -0.9797 | -1.35 | 1.5489 | 1.3182 | 2.4666 | 0.0535 | 0.0053 | 0.1544 | -0.0188 | -0.0203 | -0.098 | -0.11 | 0.0355 | -0.1199 | 0.062 | -0.0034 | -0.0091 | 0.0711 | 0.013 | 0.0776 | 5.3218 | 3.5301 | 13.6135 | 21 | 1.0333 | -0.5377 | -0.7581 | 0.8683 | 0.6474 | 1.5277 | -0.0178 | 0.0544 | -0.0106 | -0.005 | -0.0242 | 0.0107 | 0.0124 | -0.0802 | 0.0914 | 0.0536 | -0.0111 | -0.0047 | 0.064 | -0.009 | 0.0684 | -4.1414 | -2.747 | 14.5229 | 22 | 1.4883 | 0.1796 | -0.5171 | 1.3966 | 0.2579 | 2.7784 | 0.0327 | -0.272 | 0.0106 | 0.2455 | 0.0079 | -0.0845 | 0.0614 | 0.114 | -0.0358 | 0.0703 | 0.0128 | -0.0162 | 0.0922 | 0.0028 | 0.0875 | -0.6428 | -7.5899 | 27.9623 | 23 | 1.6261 | 0.058 | 0.2312 | 1.3445 | 0.401 | 1.5392 | 0.0105 | -0.4262 | 0.0508 | 0.2188 | -0.0179 | 0.0328 | 0.0776 | 0.014 | 0.0232 | 0.1272 | -0.0099 | 0.0051 | 0.1532 | 0.0003 | 0.0776 | -9.5022 | -11.9269 | 35.9196 | 24 | 1.293 | -0.0845 | -0.4688 | 0.591 | 0.1707 | 1.3847 | -0.0161 | 0.0282 | -0.1046 | -0.0247 | -0.0064 | -0.0135 | 0.0189 | 0.0126 | 0.0155 | 0.0562 | -0.0092 | -0.0061 | 0.0439 | -0.0078 | 0.067 | -4.9584 | -14.8578 | 17.1893 | 25 | 3.3228 | 1.8589 | 1.0678 | 2.0579 | 0.8576 | 2.1759 | -0.0717 | -0.421 | 0.3831 | 0.1913 | -0.3482 | 0.9268 | 0.1013 | -0.6281 | 0.2826 | 0.1764 | 0.0075 | 0.0408 | 0.2035 | -0.073 | 0.2503 | -36.8909 | 18.5935 | 21.2442 | 26 | 3.6212 | 0.2803 | -1.3483 | 2.0902 | 0.5683 | 2.7471 | -0 | 0.1577 | 0.1525 | -0.212 | 0.0246 | 0.0488 | -0.1193 | -0.0687 | -0.016 | 0.0983 | 0.0058 | -0.0154 | 0.0402 | 0.0083 | 0.0766 | -22.2522 | 23.3802 | 11.363 | 27 | 1.7434 | -0.2847 | -0.8153 | 1.6806 | -0.3223 | 0.8767 | 0.0129 | 0.0929 | 0.3651 | -0.1232 | 0.0426 | -0.0527 | -0.1935 | -0.0728 | -0.0532 | 0.1384 | 0.0086 | -0.0071 | 0.0727 | -0.0103 | 0.1431 | -18.1804 | 31.1429 | 12.8179 | 28 | 6.8901 | -4.0454 | -2.4742 | 4.1141 | 2.9305 | 2.1719 | 0.0257 | -0.0616 | 0.3205 | -0.0235 | 0.0326 | -0.1907 | -0.1568 | 0.0369 | -0.0608 | 0.1369 | -0.0238 | -0.007 | 0.0691 | -0.0098 | 0.126 | -11.152 | 28.5126 | 25.4713 | 29 | 1.3203 | -1.2099 | -1.1743 | 1.9431 | 1.2318 | 1.7692 | 0.049 | 0.0066 | 0.057 | -0.1206 | -0.0452 | -0.0836 | -0.0801 | 0.0276 | -0.0217 | 0.0709 | -0.0154 | 0.0002 | 0.0719 | -0 | 0.0693 | -9.1193 | 14.9661 | 10.4382 | 30 | 4.2123 | -2.512 | -4.5585 | 1.621 | 3.0262 | 6.0094 | 0.0012 | -0.1693 | 0.1336 | -0.0263 | 0.0974 | -0.1169 | -0.0419 | 0.1954 | -0.1313 | 0.0814 | -0.0047 | -0.0109 | 0.0542 | -0.002 | 0.0945 | -7.6564 | 16.5002 | 19.7451 | 31 | 1.048 | -0.4389 | -0.5677 | 0.6051 | 0.2951 | 0.7287 | -0.0392 | -0.0079 | 0.0113 | 0.0141 | -0.0105 | 0.0256 | 0.0322 | -0.0235 | 0.0551 | 0.0811 | -0.0081 | -0.0031 | 0.0621 | -0.0133 | 0.0756 | -14.2331 | 7.5895 | 17.1582 | 32 | 1.1354 | -0.1387 | -0.5566 | 1.0906 | 0.4612 | 1.9415 | 0.0284 | 0.1924 | 0.13 | -0.248 | -0.0317 | -0.0399 | -0.2279 | -0.0501 | -0.0207 | 0.115 | 0.0029 | -0.0027 | 0.0764 | 0.0152 | 0.0931 | -17.5918 | 12.2618 | 4.4956 | 33 | 1.8397 | 0.0126 | -0.6102 | 1.1449 | 0.0698 | 1.8069 | 0.0546 | 0.1576 | -0.0007 | -0.2544 | -0.0764 | -0.0424 | -0.094 | -0.0057 | 0.0612 | 0.1589 | 0.0086 | -0.0003 | 0.1285 | -0.0034 | 0.0699 | -21.0511 | 4.4623 | -5.5121 | 34 | 0.6386 | -0.2038 | -0.1703 | 0.5046 | 0.2715 | 1.1042 | -0.0028 | -0.0108 | 0.0377 | 0.0058 | -0.0438 | 0.033 | -0.0315 | -0.0015 | 0.049 | 0.0836 | -0.0121 | -0.0012 | 0.0846 | -0.0045 | 0.0853 | -26.0051 | 7.8991 | 13.2174 |
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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 13 )A0 - 13 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 14 through 34 )A14 - 34 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 35 through 72 )A35 - 72 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 73 through 109 )A73 - 109 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 110 through 138 )A110 - 138 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 139 through 257 )A139 - 257 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid -3 through 13 ) | B-3 - 13 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 14 through 34 )B14 - 34 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 35 through 58 )B35 - 58 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 59 through 72 )B59 - 72 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 73 through 109 )B73 - 109 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 110 through 182 )B110 - 182 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 183 through 205 )B183 - 205 | 14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 206 through | | | | | | | | | | | | | | | | | | | | | | | | | |
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