Software | Name | Version | Classification |
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PHASER | | phasingPHENIX | | refinementPDB_EXTRACT | 3.25 | data extractionxia2 | | data reductionpointless | | data scaling | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→64.21 Å / FOM work R set: 0.8877 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2029 | 2708 | 4.92 % |
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Rwork | 0.1559 | 52294 | - |
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obs | 0.1581 | 55002 | 91.08 % |
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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: 92.73 Å2 / Biso mean: 26.95 Å2 / Biso min: 8.98 Å2 |
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Refinement step | Cycle: final / Resolution: 1.85→64.21 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5050 | 0 | 6 | 506 | 5562 |
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Biso mean | - | - | 39.61 | 34.52 | - |
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Num. residues | - | - | - | - | 654 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 5284 | X-RAY DIFFRACTION | f_angle_d1.126 | 7221 | X-RAY DIFFRACTION | f_chiral_restr0.081 | 811 | X-RAY DIFFRACTION | f_plane_restr0.005 | 916 | X-RAY DIFFRACTION | f_dihedral_angle_d12.113 | 1885 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.85-1.8837 | 0.2619 | 165 | 0.2182 | 2770 | 94 | 1.8837-1.9199 | 0.2594 | 154 | 0.195 | 2809 | 94 | 1.9199-1.9591 | 0.2278 | 154 | 0.1937 | 2750 | 93 | 1.9591-2.0017 | 0.2509 | 139 | 0.1859 | 2799 | 93 | 2.0017-2.0482 | 0.2326 | 132 | 0.1774 | 2769 | 93 | 2.0482-2.0995 | 0.2386 | 156 | 0.1737 | 2742 | 92 | 2.0995-2.1562 | 0.2232 | 135 | 0.1626 | 2754 | 93 | 2.1562-2.2197 | 0.2075 | 156 | 0.1546 | 2785 | 93 | 2.2197-2.2913 | 0.1922 | 143 | 0.1592 | 2735 | 92 | 2.2913-2.3732 | 0.2402 | 140 | 0.1657 | 2749 | 92 | 2.3732-2.4683 | 0.2243 | 163 | 0.1648 | 2763 | 92 | 2.4683-2.5806 | 0.2152 | 144 | 0.1631 | 2713 | 91 | 2.5806-2.7167 | 0.2106 | 117 | 0.1545 | 2757 | 91 | 2.7167-2.8869 | 0.2044 | 144 | 0.1556 | 2734 | 91 | 2.8869-3.1098 | 0.2384 | 158 | 0.158 | 2735 | 90 | 3.1098-3.4227 | 0.1753 | 124 | 0.147 | 2715 | 89 | 3.4227-3.9179 | 0.1391 | 132 | 0.1388 | 2733 | 89 | 3.9179-4.9359 | 0.1736 | 132 | 0.1251 | 2705 | 87 | 4.9359-64.21 | 0.2116 | 120 | 0.1656 | 2777 | 84 |
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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 | 0.1333 | -0.0569 | -0.0311 | 0.0259 | -0.0129 | 0.1367 | -0.0533 | -0.0244 | -0.0389 | -0.2339 | -0.1713 | 0.085 | -0.1887 | -0.0974 | -0.2401 | 0.3721 | 0.0906 | -0.1961 | 0.1258 | -0.0177 | 0.3522 | 38.774 | 23.6416 | 28.0243 | 2 | 0.0665 | -0.0267 | 0.0119 | 0.0296 | -0.0201 | 0.024 | -0.0143 | -0.068 | 0.0639 | -0.08 | -0.0611 | 0.0164 | -0.0829 | -0.1043 | -0.037 | 0.166 | 0.2419 | -0.0973 | 0.3662 | -0.1855 | 0.3449 | 33.5309 | 19.1704 | 38.9097 | 3 | 0.0394 | 0.097 | 0.0224 | 0.3329 | 0.0646 | 0.0294 | -0.1049 | -0.0372 | 0.0595 | -0.1993 | -0.019 | 0.029 | -0.1621 | -0.0966 | -0.0337 | 0.1624 | 0.0476 | -0.0322 | 0.154 | -0.0364 | 0.1504 | 46.7418 | 18.5858 | 38.6983 | 4 | 0.0242 | 0.1033 | 0.0618 | 0.4564 | 0.2292 | 0.1356 | -0.1275 | -0.0482 | 0.0934 | -0.4154 | -0.0373 | 0.025 | -0.3506 | -0.2062 | -0.1547 | 0.3298 | 0.1829 | -0.1664 | 0.1109 | -0.09 | 0.317 | 42.3728 | 26.2599 | 35.8857 | 5 | 0.017 | -0.0129 | -0.0089 | 0.1414 | 0.0551 | 0.0446 | -0.1231 | -0.1202 | 0.0328 | -0.1666 | -0.2041 | 0.1596 | -0.0953 | -0.2169 | -0.0477 | 0.1866 | 0.0338 | -0.035 | 0.2187 | -0.045 | 0.1846 | 40.9055 | 12.1476 | 36.3793 | 6 | 0.1147 | -0.0318 | -0.0995 | 0.0094 | 0.0252 | 0.0895 | -0.0464 | 0.1173 | -0.1031 | 0.0767 | -0.0922 | 0.0201 | -0.158 | -0.0119 | -0.0253 | 0.4605 | 0.018 | -0.1279 | 0.193 | -0.0022 | 0.31 | 39.5632 | 16.8247 | 5.953 | 7 | 0.015 | -0.0024 | -0.0041 | 0.0067 | 0.0029 | 0.01 | 0.0261 | 0.0554 | -0.1037 | 0.0309 | 0.0107 | 0.0633 | -0.1643 | -0.0634 | -0.0005 | 0.391 | 0.0397 | -0.1312 | 0.1943 | 0.0018 | 0.2244 | 38.2283 | 8.4676 | 3.5664 | 8 | 0.001 | -0.0045 | -0.0009 | 0.0096 | 0.0034 | 0.0089 | -0.0609 | 0.0346 | -0.0356 | 0.1015 | -0.1151 | -0.0027 | -0.2992 | -0.1251 | 0.0001 | 0.4104 | -0.005 | -0.0303 | 0.2347 | -0.0231 | 0.3246 | 35.1601 | 12.9215 | 12.5211 | 9 | 0.0464 | -0.0383 | -0.0195 | 0.0291 | 0.0248 | 0.0641 | -0.0392 | -0.0355 | -0.0107 | 0.0093 | 0.0019 | -0.0561 | -0.2909 | -0.0291 | -0 | 0.3126 | -0.0075 | -0.057 | 0.2022 | -0.025 | 0.2233 | 40.8914 | 8.7167 | 8.7916 | 10 | 0.0013 | 0.0019 | -0.0016 | 0.0239 | -0.0412 | 0.0676 | 0.0224 | 0.2034 | -0.0499 | 0.1353 | 0.1042 | 0.1316 | -0.2517 | -0.2535 | 0.0132 | 0.3242 | 0.0465 | -0.0786 | 0.3206 | -0.0899 | 0.3298 | 29.3045 | 6.9336 | 4.8991 | 11 | 0.0061 | 0.0031 | 0.0051 | 0.0023 | 0.0038 | 0.0043 | 0.0826 | 0.1671 | -0.0098 | 0.086 | 0.0161 | 0.022 | -0.0768 | 0.0144 | 0 | 0.377 | 0.0824 | -0.114 | 0.3186 | -0.0601 | 0.3744 | 29.6436 | 12.4122 | 1.838 | 12 | 0.1733 | -0.0963 | -0.0857 | 0.1842 | 0.0574 | 0.1203 | 0.0019 | -0.0201 | 0.0199 | -0.0285 | -0.0123 | 0.0124 | 0.0053 | -0.0023 | -0 | 0.1151 | 0.0006 | -0.0174 | 0.1129 | -0.024 | 0.1271 | 51.5737 | -0.0426 | 35.0034 | 13 | 0.1153 | 0.0396 | 0.0957 | 0.176 | 0.0942 | 0.1 | -0.0244 | 0.132 | 0.1319 | -0.1256 | -0.0008 | -0.0756 | -0.2548 | 0.0394 | -0.0008 | 0.2712 | 0.0118 | -0.0286 | 0.1967 | 0.0498 | 0.1384 | 48.9606 | 5.0036 | -1.2318 | 14 | 0.0096 | -0.0152 | -0.015 | 0.0257 | 0.0261 | 0.0227 | -0.0048 | 0.0448 | 0.0156 | 0.0477 | -0.0685 | 0.1173 | 0.0273 | -0.1336 | 0.0001 | 0.2241 | 0.0189 | 0.0392 | 0.2967 | -0.017 | 0.1835 | 45.1398 | 19.0583 | 78.1385 | 15 | -0.001 | 0.0079 | 0.0102 | 0.0232 | 0.0037 | 0.0348 | 0.0552 | -0.0111 | -0.1762 | 0.0956 | -0.0889 | 0.1026 | 0.1001 | -0.2535 | -0.0006 | 0.1078 | -0.0332 | 0.0089 | 0.2895 | -0.0159 | 0.1781 | 40.3916 | 13.6534 | 66.5065 | 16 | 0.025 | -0.024 | -0.0074 | 0.0191 | 0.003 | 0.0125 | -0.0008 | 0.0154 | 0.0758 | -0.0219 | 0.0332 | -0.1015 | -0.1106 | -0.0263 | 0 | 0.1577 | -0.0209 | 0.012 | 0.1776 | 0.0002 | 0.177 | 52.9758 | 17.8885 | 69.0891 | 17 | 0.0008 | 0.0037 | -0.0078 | 0.0079 | -0.0169 | 0.0309 | -0.0514 | -0.101 | -0.1131 | -0.0134 | 0.0381 | 0.0043 | 0.0801 | -0.0006 | 0 | 0.1466 | -0.0401 | 0.0044 | 0.1198 | 0.0021 | 0.1361 | 51.0834 | 9.9136 | 65.3272 | 18 | 0.0078 | -0.0092 | 0.0016 | 0.0083 | -0.001 | 0.0093 | -0.0955 | 0.0396 | -0.1031 | 0.0067 | -0.0394 | 0.0121 | 0.0788 | -0.0285 | 0.0001 | 0.19 | 0.0101 | 0.0057 | 0.1947 | 0.0073 | 0.1858 | 58.6077 | 8.5348 | 70.6656 | 19 | 0.0007 | -0.003 | 0.001 | 0.0085 | -0.0117 | 0.0137 | 0.006 | -0.0241 | -0.0406 | 0.1265 | -0.0802 | 0.0497 | 0.0798 | -0.1984 | 0 | 0.16 | -0.0607 | 0.0371 | 0.2484 | 0.0078 | 0.175 | 43.668 | 8.9857 | 72.4105 | 20 | 0.0655 | 0.013 | -0.0616 | 0.0662 | -0.0057 | 0.0468 | -0.0151 | -0.0214 | -0.0761 | 0.0496 | -0.0499 | -0.0185 | 0.0261 | 0.0239 | -0 | 0.1171 | 0.002 | -0.002 | 0.1498 | -0.0192 | 0.1179 | 50.7585 | 18.4808 | 66.4437 | 21 | 0.008 | -0.004 | 0.0052 | 0.0057 | -0.0051 | 0.0195 | 0.0156 | 0.0339 | -0.0089 | 0.0251 | -0.0319 | 0.0421 | -0.0155 | -0.0041 | 0.0001 | 0.2549 | 0.0204 | 0.0123 | 0.208 | -0.0105 | 0.0985 | 51.6419 | 21.5816 | 83.3401 | 22 | 0.0003 | -0.0007 | -0.0037 | 0.0082 | -0.0134 | 0.0289 | 0.0075 | -0.0712 | -0.0344 | 0.0408 | 0.0087 | -0.0434 | -0.0907 | 0.0362 | -0 | 0.127 | -0.01 | -0.0084 | 0.1659 | -0.0012 | 0.1764 | 66.5669 | 27.8636 | 62.9097 | 23 | 0.0271 | 0.0107 | 0.018 | 0.0029 | 0.0067 | 0.0062 | 0.0603 | -0.1389 | -0.0038 | -0.007 | -0.0127 | -0.0198 | 0.0522 | 0.0952 | -0 | 0.1241 | 0.0208 | 0.0081 | 0.1125 | -0.0028 | 0.17 | 63.0625 | 37.5864 | 56.6911 | 24 | 0.0159 | 0.0103 | -0.0049 | 0.046 | -0.0323 | 0.0171 | 0.0049 | 0.0579 | -0.0567 | 0.0571 | -0.0188 | 0.0577 | -0.0665 | 0.0324 | 0.0236 | 0.0855 | 0.0202 | 0.0096 | 0.1262 | -0.014 | 0.1643 | 59.958 | 23.367 | 56.0323 | 25 | 0.0006 | -0.0023 | -0.0035 | 0.0088 | -0.002 | 0.0144 | 0.0284 | -0.1737 | 0.1101 | 0.0235 | -0.0174 | 0.0871 | -0.0107 | -0.1045 | 0.0096 | 0.1254 | 0.0016 | 0.0275 | 0.2249 | -0.0576 | 0.1217 | 49.8042 | 31.0029 | 64.4894 | 26 | 0.0046 | 0.0005 | 0.001 | 0.011 | 0.005 | -0.0005 | -0.1126 | 0.0642 | 0.0131 | -0.0835 | -0.0164 | 0.1813 | -0.0536 | 0.0419 | 0 | 0.12 | 0.0067 | -0.0103 | 0.1593 | -0.0122 | 0.1836 | 52.2307 | 31.3569 | 51.0503 | 27 | 0.0294 | 0.0316 | 0.0036 | 0.0303 | -0.0011 | 0.0122 | -0.0179 | 0.0602 | -0.0301 | 0.0442 | -0.0197 | 0.0757 | -0.0674 | -0.0382 | 0 | 0.1235 | 0.0269 | 0.0124 | 0.1241 | -0.003 | 0.1361 | 57.6982 | 37.0632 | 56.2277 | 28 | 0.0055 | 0.0006 | 0.0027 | 0.0055 | 0.0032 | 0.0011 | 0.0847 | 0.0274 | -0.0052 | 0.0312 | -0.0319 | -0.0384 | -0.0367 | 0.0849 | 0 | 0.1138 | -0.013 | 0.0069 | 0.118 | -0.0064 | 0.1453 | 58.1397 | 28.4064 | 62.3453 | 29 | 0.0222 | 0.0231 | -0.0513 | 0.0248 | -0.0654 | 0.2269 | 0.0316 | -0.0506 | -0.0679 | -0.0073 | -0.0501 | 0.0429 | -0.0338 | 0.1487 | -0.0078 | 0.0791 | 0.0149 | -0.0013 | 0.1103 | -0.0206 | 0.1489 | 60.2445 | 22.8869 | 61.6133 |
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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 'H' and (resid 1 through 17 )H1 - 17 | 2 | X-RAY DIFFRACTION | 2 | chain 'H' and (resid 18 through 32 )H18 - 32 | 3 | X-RAY DIFFRACTION | 3 | chain 'H' and (resid 33 through 63 )H33 - 63 | 4 | X-RAY DIFFRACTION | 4 | chain 'H' and (resid 64 through 87 )H64 - 87 | 5 | X-RAY DIFFRACTION | 5 | chain 'H' and (resid 88 through 109 )H88 - 109 | 6 | X-RAY DIFFRACTION | 6 | chain 'H' and (resid 110 through 134 )H110 - 134 | 7 | X-RAY DIFFRACTION | 7 | chain 'H' and (resid 135 through 145 )H135 - 145 | 8 | X-RAY DIFFRACTION | 8 | chain 'H' and (resid 146 through 157 )H146 - 157 | 9 | X-RAY DIFFRACTION | 9 | chain 'H' and (resid 158 through 184 )H158 - 184 | 10 | X-RAY DIFFRACTION | 10 | chain 'H' and (resid 185 through 202 )H185 - 202 | 11 | X-RAY DIFFRACTION | 11 | chain 'H' and (resid 203 through 213 )H203 - 213 | 12 | X-RAY DIFFRACTION | 12 | chain 'L' and (resid 1 through 113 )L1 - 113 | 13 | X-RAY DIFFRACTION | 13 | chain 'L' and (resid 114 through 211 )L | | | | | | | | | | | | | | | | | | | | | | | | | |
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