Software | Name | Version | Classification |
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XDS | | data reductionXSCALE | | data scalingMOLREP | | phasingPHENIX | 1.19rc4-4035 | refinementPDB_EXTRACT | 3.27 | data extraction | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3enq Resolution: 1.45→45.58 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.16 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1631 | 2021 | 1.84 % |
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Rwork | 0.1492 | 108092 | - |
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obs | 0.1495 | 110113 | 99.92 % |
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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: 53.55 Å2 / Biso mean: 19.289 Å2 / Biso min: 2.42 Å2 |
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Refinement step | Cycle: final / Resolution: 1.45→45.58 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3257 | 0 | 45 | 730 | 4032 |
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Biso mean | - | - | 25.64 | 31.93 | - |
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Num. residues | - | - | - | - | 431 |
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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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1.45-1.49 | 0.2153 | 135 | 0.1915 | 7627 | 7762 | 100 | 1.49-1.53 | 0.2101 | 133 | 0.177 | 7640 | 7773 | 100 | 1.53-1.57 | 0.1812 | 146 | 0.1605 | 7635 | 7781 | 100 | 1.57-1.62 | 0.1486 | 158 | 0.1513 | 7609 | 7767 | 100 | 1.62-1.68 | 0.1589 | 156 | 0.1478 | 7637 | 7793 | 100 | 1.68-1.75 | 0.1618 | 155 | 0.1386 | 7634 | 7789 | 100 | 1.75-1.83 | 0.158 | 144 | 0.1392 | 7663 | 7807 | 100 | 1.83-1.92 | 0.1493 | 143 | 0.1449 | 7678 | 7821 | 100 | 1.92-2.04 | 0.1636 | 136 | 0.1437 | 7703 | 7839 | 100 | 2.04-2.2 | 0.1487 | 132 | 0.1409 | 7744 | 7876 | 100 | 2.2-2.42 | 0.147 | 131 | 0.1468 | 7766 | 7897 | 100 | 2.42-2.77 | 0.1826 | 133 | 0.1571 | 7804 | 7937 | 100 | 2.77-3.49 | 0.1624 | 155 | 0.1493 | 7844 | 7999 | 100 | 3.49-45.58 | 0.1621 | 164 | 0.1472 | 8108 | 8272 | 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 | 1.3919 | 0.5909 | 0.3642 | 2.5319 | -0.1263 | 1.2884 | -0.0262 | 0.0932 | 0.0127 | -0.1172 | -0.0068 | -0.0015 | -0.0287 | 0.0746 | 0.0336 | 0.0636 | -0.0017 | -0.0082 | 0.1187 | 0.0241 | 0.0981 | -49.0987 | 31.6009 | -22.0899 | 2 | 0.6869 | -0.3089 | 0.6805 | 1.3458 | -1.8863 | 3.7131 | -0.072 | 0.0939 | 0.1626 | 0.1057 | -0.1046 | -0.1061 | -0.259 | 0.3088 | 0.1825 | 0.1125 | -0.0312 | -0.0093 | 0.1141 | 0.0226 | 0.1331 | -38.5521 | 36.831 | -10.1068 | 3 | 0.5288 | -0.017 | 0.2834 | 0.9957 | 0.2882 | 2.4051 | -0.0282 | 0.054 | 0.1018 | -0.0002 | -0.0044 | -0.0792 | -0.1335 | 0.2161 | 0.018 | 0.0739 | -0.0192 | -0.0011 | 0.1189 | 0.028 | 0.1181 | -40.0904 | 32.3688 | -11.7521 | 4 | 0.7874 | 0.4313 | 1.7902 | 8.4706 | 0.2837 | 6.6163 | 0.0541 | 0.4545 | 0.4813 | -0.4668 | -0.0518 | 0.0346 | -0.4854 | -0.1667 | 0.0128 | 0.1364 | 0.0106 | 0.02 | 0.1838 | 0.0931 | 0.2073 | -51.5138 | 41.146 | -33.7905 | 5 | 8.4012 | 5.422 | 2.4531 | 6.2946 | 3.1612 | 5.7825 | 0.1991 | -0.5093 | -0.5012 | 0.7274 | -0.2063 | -0.0477 | 0.6015 | 0.0142 | 0.0304 | 0.1995 | 0.064 | 0.0209 | 0.216 | 0.06 | 0.1574 | -29.8287 | 5.2078 | 16.3322 | 6 | 3.1421 | 0.5543 | 1.2018 | 4.8293 | 0.9796 | 4.5203 | -0.1202 | -0.1619 | 0.09 | 0.2241 | 0.1221 | -0.4398 | -0.2711 | 0.445 | -0.0238 | 0.1336 | -0.0152 | -0.0091 | 0.1734 | -0.0102 | 0.1067 | -30.8687 | 19.6207 | 15.3066 | 7 | 5.3334 | 1.6961 | 1.5769 | 7.3007 | 4.888 | 8.5016 | 0.0328 | -0.5366 | -0.0252 | 0.6305 | -0.0558 | -0.2746 | 0.3521 | 0.2491 | 0.0041 | 0.1439 | 0.0158 | -0.0037 | 0.1887 | 0.0359 | 0.0986 | -34.403 | 12.9508 | 20.4841 | 8 | 6.8742 | 2.953 | -0.0774 | 4.7448 | 0.4448 | 5.2152 | 0.0559 | -0.1312 | -0.0701 | 0.1283 | -0.0116 | 0.0885 | -0.0265 | -0.0413 | -0.0302 | 0.0663 | 0.0107 | 0.0202 | 0.063 | -0.0075 | 0.0717 | -42.3961 | 18.697 | 16.0928 | 9 | 1.9699 | 1.1672 | -1.0199 | 3.5767 | -3.1746 | 2.917 | 0.1776 | -0.1427 | 0.0895 | 0.3775 | -0.0701 | 0.0626 | -0.4236 | 0.0058 | -0.1154 | 0.1664 | -0.0366 | -0.009 | 0.1426 | -0.0319 | 0.0996 | -35.8273 | 27.1758 | 12.9685 | 10 | 0.6979 | -0.4074 | 0.2913 | 1.0801 | 0.0381 | 1.0972 | 0.0076 | -0.0142 | -0.0524 | 0.04 | 0.011 | 0.0044 | 0.0657 | 0.0629 | -0.0213 | 0.0675 | -0.007 | 0.0098 | 0.0995 | 0.0086 | 0.0772 | -34.8718 | 10.6829 | 1.0625 | 11 | 7.1072 | -7.2541 | -3.4971 | 8.3344 | 3.3465 | 4.0424 | 0.2913 | 0.1558 | -0.0319 | -0.376 | -0.145 | 0.1061 | 0.0503 | 0.0111 | -0.0936 | 0.1083 | -0.0041 | -0.037 | 0.1253 | 0.0109 | 0.1034 | -48.5238 | 13.3712 | -16.1762 | 12 | 2.0687 | 1.0916 | 1.0764 | 4.9676 | 2.7328 | 3.4928 | 0.0781 | -0.0938 | -0.0963 | -0.0152 | -0.18 | 0.3188 | 0.1415 | -0.2326 | 0.1128 | 0.0691 | -0.0056 | -0.0084 | 0.1072 | 0.0282 | 0.1057 | -51.0207 | 11.4038 | -4.5356 | 13 | 3.8197 | -1.4571 | 0.2216 | 2.9686 | 0.159 | 0.4732 | -0.005 | 0.2046 | -0.0606 | -0.2099 | -0.0141 | -0.0844 | 0.0545 | 0.063 | 0.0243 | 0.092 | 0.0057 | -0.0101 | 0.106 | -0.0152 | 0.0309 | -38.2036 | 10.6 | -11.4725 | 14 | 9.2035 | -1.5502 | 4.2968 | 0.8163 | -0.9875 | 2.639 | -0.0213 | -0.0362 | 0.0562 | -0.0397 | -0.0117 | -0.0239 | -0.062 | 0.0295 | 0.0472 | 0.0888 | 0.0014 | 0.012 | 0.1051 | 0.0018 | 0.0809 | -35.1969 | 16.5935 | -5.424 | 15 | 4.7413 | 0.4222 | 1.507 | 7.0169 | -3.0712 | 4.9925 | -0.0781 | -0.2313 | -0.4618 | 0.3973 | 0.0051 | -0.5537 | 0.3152 | 0.3849 | 0.1048 | 0.1865 | 0.0595 | -0.0127 | 0.1798 | 0.0194 | 0.1596 | -24.3243 | 3.4027 | 9.9613 | 16 | 3.8895 | 0.9957 | 0.8404 | 3.0195 | 4.8268 | 8.235 | -0.0325 | 0.1911 | 0.5184 | -0.3586 | -0.0705 | 0.3994 | -0.624 | -0.3377 | 0.0931 | 0.1465 | 0.0297 | 0.0256 | 0.1753 | 0.083 | 0.1839 | -58.4544 | 41.7668 | -29.7132 | 17 | 3.0205 | 0.4733 | 1.7469 | 1.9897 | 0.4194 | 2.3671 | 0.0432 | -0.0785 | -0.0232 | 0.0576 | 0.0003 | 0.07 | 0.0301 | -0.1509 | -0.0416 | 0.0618 | -0.0012 | 0.0155 | 0.1216 | 0.0163 | 0.0997 | -64.2372 | 32.1473 | -22.134 | 18 | 0.4593 | -1.114 | 0.4297 | 3.2524 | -1.3367 | 1.608 | 0.0118 | -0.1615 | -0.2078 | 0.0246 | 0.1268 | 0.3113 | 0.1192 | -0.1406 | -0.1303 | 0.0926 | -0.0358 | -0.037 | 0.1605 | 0.0259 | 0.1568 | -62.339 | 21.1592 | -19.4251 |
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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 76 through 115 )B76 - 115 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 116 through 149 )B116 - 149 | 3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resid 150 through 203 )B150 - 203 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 204 through 215 )B204 - 215 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 1 through 15 )A1 - 15 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 16 through 27 )A16 - 27 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 28 through 43 )A28 - 43 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 44 through 61 )A44 - 61 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 62 through 75 )A62 - 75 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 76 through 134 )A76 - 134 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 135 through 149 )A135 - 149 | 12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resid 150 through 165 )A150 - 165 | 13 | X-RAY DIFFRACTION | 13 | chain 'A' and (resid 166 through 187 )A | | | | | | | | | | | | | | | | | | | | | | | | | |
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