Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement |
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Refinement | Method to determine structure: SAD / Resolution: 2.702→40.794 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 19.81 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1913 | 3168 | 5.37 % | Random |
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Rwork | 0.1594 | - | - | - |
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all | 0.1611 | 39742 | - | - |
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obs | 0.1611 | 36574 | 74.64 % | - |
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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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Refinement step | Cycle: LAST / Resolution: 2.702→40.794 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4953 | 0 | 80 | 172 | 5205 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 5096 | X-RAY DIFFRACTION | f_angle_d1.188 | 6906 | X-RAY DIFFRACTION | f_dihedral_angle_d12.823 | 1787 | X-RAY DIFFRACTION | f_chiral_restr0.045 | 795 | X-RAY DIFFRACTION | f_plane_restr0.005 | 901 | | | | | |
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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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2.7019-2.7422 | 0.257 | 11 | 0.2477 | 201 | X-RAY DIFFRACTION | 6 | 2.7422-2.7851 | 0.3352 | 25 | 0.2714 | 436 | X-RAY DIFFRACTION | 13 | 2.7851-2.8307 | 0.3512 | 49 | 0.2577 | 897 | X-RAY DIFFRACTION | 27 | 2.8307-2.8795 | 0.314 | 77 | 0.29 | 1332 | X-RAY DIFFRACTION | 41 | 2.8795-2.9319 | 0.2704 | 98 | 0.2554 | 1724 | X-RAY DIFFRACTION | 52 | 2.9319-2.9882 | 0.3044 | 107 | 0.2487 | 1890 | X-RAY DIFFRACTION | 58 | 2.9882-3.0492 | 0.3152 | 115 | 0.2418 | 2008 | X-RAY DIFFRACTION | 62 | 3.0492-3.1155 | 0.2412 | 133 | 0.2022 | 2351 | X-RAY DIFFRACTION | 72 | 3.1155-3.1879 | 0.2201 | 138 | 0.2006 | 2451 | X-RAY DIFFRACTION | 75 | 3.1879-3.2676 | 0.2262 | 151 | 0.1896 | 2592 | X-RAY DIFFRACTION | 80 | 3.2676-3.3559 | 0.2434 | 153 | 0.1849 | 2687 | X-RAY DIFFRACTION | 83 | 3.3559-3.4546 | 0.1924 | 167 | 0.1816 | 2807 | X-RAY DIFFRACTION | 86 | 3.4546-3.5661 | 0.1649 | 168 | 0.1683 | 2871 | X-RAY DIFFRACTION | 89 | 3.5661-3.6935 | 0.163 | 170 | 0.1599 | 3000 | X-RAY DIFFRACTION | 92 | 3.6935-3.8412 | 0.2368 | 167 | 0.1574 | 3065 | X-RAY DIFFRACTION | 93 | 3.8412-4.0159 | 0.1634 | 173 | 0.1419 | 3100 | X-RAY DIFFRACTION | 96 | 4.0159-4.2274 | 0.1938 | 175 | 0.1269 | 3153 | X-RAY DIFFRACTION | 97 | 4.2274-4.492 | 0.1482 | 185 | 0.1206 | 3182 | X-RAY DIFFRACTION | 98 | 4.492-4.8383 | 0.1505 | 181 | 0.1184 | 3176 | X-RAY DIFFRACTION | 98 | 4.8383-5.3243 | 0.1695 | 180 | 0.129 | 3199 | X-RAY DIFFRACTION | 99 | 5.3243-6.0925 | 0.213 | 180 | 0.151 | 3259 | X-RAY DIFFRACTION | 99 | 6.0925-7.6676 | 0.1607 | 183 | 0.1444 | 3246 | X-RAY DIFFRACTION | 100 | 7.6676-40.7983 | 0.157 | 182 | 0.1512 | 3247 | X-RAY DIFFRACTION | 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 | 5.1015 | -3.4215 | -4.7921 | 5.9871 | 2.9451 | 7.6451 | -0.1232 | 0.4554 | -0.558 | -0.5131 | -0.1401 | 0.3631 | 0.3955 | -0.059 | 0.2859 | 0.3385 | 0.0102 | -0.1083 | 0.4712 | -0.0908 | 0.2261 | 152.1693 | 54.7587 | 35.1298 | 2 | 0.9353 | 0.9304 | 0.7166 | 2.9013 | -0.451 | 1.2478 | 0.0745 | 0.1306 | 0.0972 | 0.3237 | 0.0334 | 0.2417 | 0.085 | -0.2007 | -0.0929 | 0.1949 | 0.0792 | 0.0433 | 0.2229 | 0.0082 | 0.1356 | 157.2659 | 67.7004 | 47.3287 | 3 | 5.3253 | -1.8002 | -2.0081 | 8.2908 | -1.1622 | 5.1142 | 0.1643 | -0.266 | 0.2846 | 0.3288 | 0.164 | -0.6414 | -0.1416 | 0.4918 | -0.3326 | 0.2561 | 0.0721 | -0.0104 | 0.1956 | -0.1114 | 0.2164 | 167.2822 | 62.9014 | 47.5254 | 4 | 6.2499 | -2.5985 | 4.9139 | 3.9364 | -0.5443 | 4.8448 | 0.0841 | 0.7899 | -0.1368 | -0.4939 | 0.4606 | -0.8047 | 0.8445 | 1.1993 | -0.5549 | 0.4786 | 0.1912 | 0.026 | 0.5357 | -0.0155 | 0.3178 | 169.2309 | 61.9666 | 39.6482 | 5 | 1.2135 | -0.7096 | -0.7472 | 1.0873 | 0.716 | 0.6279 | -0.0223 | -0.1595 | 0.1562 | 0.0326 | 0.1113 | 0.1822 | -0.0361 | -0.1511 | -0.0329 | 0.1708 | 0.1306 | 0.0162 | 0.2689 | 0.0795 | 0.2182 | 151.7729 | 70.2731 | 43.7367 | 6 | 6.2751 | 5.6771 | 3.5666 | 5.2818 | 3.8949 | 5.0904 | 0.4605 | 1.1855 | -2.1244 | 0.1773 | 0.3721 | -0.9898 | 2.0224 | 0.28 | -0.8214 | 0.6156 | 0.1146 | -0.2092 | 0.4668 | -0.1778 | 0.6661 | 157.2503 | 50.647 | 32.8308 | 7 | 3.755 | 2.0774 | -0.023 | 5.6578 | -0.6372 | 1.7098 | 0.1184 | 0.3141 | -0.0905 | -0.0825 | -0.0039 | -0.3544 | 0.1071 | -0.0559 | -0.1217 | 0.1805 | 0.0781 | -0.0174 | 0.3602 | 0.0529 | 0.0437 | 161.885 | 72.6031 | 29.9463 | 8 | 0.4389 | 0.5383 | 0.0841 | 5.3331 | 3.5783 | 4.3157 | -0.1092 | 0.1328 | 0.0087 | -0.3517 | -0.0096 | -0.186 | -0.0513 | 0.7026 | 0.1453 | 0.2204 | 0.0743 | 0.0207 | 0.418 | 0.1079 | 0.1283 | 162.9377 | 83.0584 | 23.9538 | 9 | 2.4319 | 2.5381 | 1.9019 | 6.3175 | 3.6609 | 5.8183 | -0.1364 | 0.6323 | 0.0261 | -0.8335 | 0.2353 | -0.009 | 0.1278 | 0.0002 | -0.0525 | 0.2948 | 0.1073 | -0.0009 | 0.4741 | 0.0167 | 0.1232 | 159.9881 | 67.654 | 22.3823 | 10 | 4.4329 | 1.4332 | 2.1777 | 4.9267 | 1.2305 | 6.2664 | -0.0051 | 0.6749 | -0.166 | -0.8524 | 0.0553 | 0.5039 | 0.1326 | -0.5946 | -0.05 | 0.3509 | 0.0541 | -0.151 | 0.5162 | 0.0463 | 0.2496 | 150.4937 | 67.8243 | 24.505 | 11 | 5.749 | 4.6202 | -2.1232 | 8.8546 | -1.9656 | 3.5311 | 0.3759 | 0.0558 | 0.3128 | 0.1761 | -0.4853 | -0.6241 | -0.6649 | 0.4937 | 0.2023 | 0.2952 | 0.0369 | -0.0373 | 0.2649 | 0.1795 | 0.3172 | 167.6194 | 89.6914 | 37.5361 | 12 | 1.1065 | 1.553 | -0.8104 | 3.7106 | -2.8685 | 6.4955 | -0.0919 | 0.4269 | 0.6628 | -0.2157 | -0.0723 | 0.0967 | -0.5423 | -0.0719 | 0.1698 | 0.3836 | 0.1451 | -0.0189 | 0.3252 | 0.1587 | 0.4256 | 159.6965 | 93.0954 | 35.2907 | 13 | 3.7781 | -2.0301 | 2.7134 | 4.9104 | -1.525 | 2.2126 | -0.1752 | -0.4096 | -0.0529 | 0.253 | 0.1213 | 0.0104 | -0.0811 | -0.1911 | 0.0577 | 0.1762 | 0.1026 | -0.0221 | 0.2297 | 0.1055 | 0.1794 | 155.7518 | 85.5212 | 34.57 | 14 | 2.0057 | -1.7157 | 2.8039 | 7.0408 | -0.038 | 7.0068 | -0.0431 | 0.5688 | 0.2185 | -0.8759 | -0.0303 | 0.0088 | -0.0534 | 0.4425 | 0.0841 | 0.2637 | 0.0447 | -0.0469 | 0.4993 | 0.0695 | 0.1556 | 154.617 | 78.5124 | 19.913 | 15 | 0.4691 | 0.0043 | 0.576 | 0.5355 | -0.1124 | 0.7342 | -0.0786 | 0.0867 | 0.1768 | -0.2718 | -0.0111 | 0.2611 | -0.1347 | -0.0744 | 0.1362 | 0.237 | 0.1383 | -0.0591 | 0.401 | 0.1461 | 0.2347 | 153.9426 | 82.6361 | 27.6626 | 16 | 1.8872 | -0.1345 | 0.2268 | 2.6364 | -1.3642 | 0.7197 | 0.0271 | 0.2291 | -0.1281 | -0.5474 | 0.0797 | 0.4276 | 0.2005 | -0.2826 | -0.0847 | 0.2513 | 0.0089 | -0.0863 | 0.486 | -0.0485 | 0.1866 | 149.4094 | 63.8573 | 28.505 | 17 | 3.8534 | -1.3424 | 1.036 | 5.3705 | 1.2491 | 2.3288 | 0.0459 | 0.2205 | -0.217 | -0.2507 | 0.096 | 1.0672 | 0.057 | -0.8588 | -0.1232 | 0.2034 | 0.0231 | -0.0206 | 0.595 | 0.0449 | 0.3858 | 137.8404 | 69.6186 | 34.3325 | 18 | 3.0757 | 0.0981 | 2.8243 | 3.4376 | -0.0028 | 2.5961 | -0.0718 | 0.1912 | 0.4223 | -0.1407 | -0.1462 | 0.2879 | -0.0545 | 0.0302 | 0.2056 | 0.3913 | 0.3026 | 0.0339 | 0.6356 | 0.1167 | 0.3875 | 135.9124 | 90.468 | 35.5893 | 19 | 2.4198 | -0.352 | -0.111 | 2.3349 | 0.4107 | 0.683 | -0.0056 | -0.0633 | 0.1575 | -0.0119 | -0.0307 | 0.2533 | -0.1212 | -0.2035 | 0.0523 | 0.1844 | 0.1856 | 0.0582 | 0.4081 | 0.0476 | 0.3222 | 142.0146 | 79.0811 | 42.7361 | 20 | 3.3747 | -1.1817 | 0.7497 | 0.4375 | -0.452 | 1.6781 | 0.0187 | -0.2179 | -0.1824 | -0.1937 | 0.0387 | 0.5085 | 0.0732 | -0.3863 | -0.085 | 0.151 | 0.0599 | -0.0706 | 0.5222 | 0.0513 | 0.2342 | 142.3012 | 70.7365 | 30.571 | 21 | 4.5204 | -5.4721 | -1.3861 | 7.1202 | 2.8611 | 4.5565 | -0.3368 | -0.6414 | 0.2499 | 0.2452 | 0.0964 | 0.9793 | 0.0887 | -0.6135 | 0.2561 | 0.5377 | 0.398 | 0.004 | 1.3454 | 0.1592 | 1.1649 | 108.2314 | 91.8005 | 43.89 | 22 | 0.122 | 0.1582 | 0.0387 | 0.2641 | -0.0124 | 0.0845 | 0.0283 | 0.102 | 0.0686 | -0.0683 | -0.0867 | 0.5121 | -0.1024 | -0.1662 | 0.0265 | 0.5764 | 0.5479 | 0.0718 | 0.7922 | 0.085 | 0.7898 | 124.6656 | 99.8248 | 48.0831 | 23 | 4.1903 | -1.4668 | -2.8785 | 2.5437 | 2.2196 | 3.2244 | 0.1701 | 0.2694 | -0.0177 | -0.302 | -0.0931 | -0.2753 | 0.1725 | 0.3227 | -0.0998 | 0.6766 | 0.449 | 0.06 | 0.7062 | -0.0243 | 1.0512 | 116.3372 | 108.4935 | 51.3577 | 24 | 2.7635 | -0.1828 | 0.7046 | 2.5742 | -0.1119 | 0.4501 | -0.0715 | -0.1539 | 0.2489 | 0.112 | -0.0141 | 0.3304 | -0.0972 | -0.1353 | 0.0902 | 0.5257 | 0.4105 | 0.0808 | 0.6855 | 0.0742 | 0.6684 | 125.4267 | 94.3263 | 49.9571 | 25 | 1.0112 | -0.5492 | 0.0225 | 0.7434 | -0.0012 | 0.0004 | -0.0659 | -0.0019 | 0.2112 | 0.1085 | -0.055 | 0.3692 | -0.1393 | -0.3299 | 0.1682 | 0.6115 | 0.4266 | 0.2581 | 1.0446 | -0.0266 | 1.1247 | 115.5489 | 93.324 | 58.9389 | 26 | 5.1227 | -1.7293 | 0.0387 | 2.3513 | 2.0258 | 3.3032 | -0.4332 | -0.5888 | -0.3404 | 0.3866 | -0.1775 | 0.3317 | 0.4916 | -0.6424 | 0.613 | 1.0241 | 0.3509 | 0.4729 | 1.1281 | -0.0487 | 0.8655 | 121.6636 | 87.203 | 73.6402 | 27 | 8.1867 | -0.0445 | -1.8147 | 2.2577 | -1.478 | 3.102 | 0.0005 | -0.5808 | 0.3173 | 0.2674 | -0.1072 | 0.3069 | 0.0656 | -0.0632 | 0.0907 | 0.7511 | 0.338 | 0.4162 | 1.2983 | -0.0741 | 1.0579 | 112.2462 | 88.4652 | 66.6766 | 28 | 6.5732 | 1.4898 | -1.3806 | 1.3366 | -0.6183 | 1.555 | -0.3924 | -0.2343 | -0.8092 | 0.0826 | 0.2907 | -0.534 | 0.2793 | 0.1933 | 0.086 | 0.7712 | 0.4288 | 0.4048 | 1.7038 | 0.2054 | 1.5477 | 105.3952 | 84.3883 | 59.7143 | 29 | 8.0794 | -2.7809 | 3.4509 | 7.5334 | 0.9208 | 4.4976 | 0.0292 | 0.1182 | -0.6393 | 0.3179 | 0.0779 | 0.9606 | 0.0841 | -1.0192 | -0.0919 | 0.5624 | 0.3423 | 0.2231 | 1.4348 | 0.2097 | 1.1586 | 111.706 | 79.4193 | 56.3066 | 30 | 4.5465 | 0.1557 | 2.1603 | 0.0168 | 0.035 | 1.1579 | -0.1373 | -0.1928 | 0.5112 | 0.0118 | -0.0509 | 0.131 | -0.1318 | -0.158 | 0.1898 | 0.8283 | 0.4883 | 0.1272 | 0.7825 | 0.0146 | 0.7537 | 130.1289 | 94.3766 | 64.9135 | 31 | 1.1271 | -1.2965 | -2.584 | 4.3873 | 6.2786 | 9.8679 | -0.1423 | -0.3968 | 0.3128 | 0.3737 | 0.0389 | 0.4413 | -0.5112 | -0.745 | 0.098 | 1.1448 | 0.4918 | 0.3233 | 0.9202 | -0.0085 | 0.9726 | 135.1904 | 98.6145 | 77.4154 | 32 | 5.5182 | -2.7207 | -0.8164 | 2.5687 | 1.9337 | 2.6629 | -0.0281 | -0.0541 | 0.2488 | 0.197 | 0.0884 | -0.1088 | 0.1082 | 0.0847 | -0.0803 | 0.9077 | 0.4409 | 0.1323 | 0.6199 | 0.0689 | 0.5592 | 136.2319 | 89.1813 | 69.6444 | 33 | 0.0971 | -0.2151 | 0.0973 | 0.5809 | 0.1254 | 1.2093 | -0.1344 | -0.0693 | -0.3083 | 0.2799 | -0.0606 | 0.6002 | -0.0286 | -0.6267 | 0.2301 | 0.568 | 0.3198 | 0.2697 | 0.8878 | 0.0462 | 0.7431 | 122.8767 | 83.2628 | 66.264 | 34 | 6.1318 | 1.0813 | 5.9351 | 0.2022 | 1.1204 | 6.2123 | 0.0022 | -0.4392 | 0.1096 | 0.2886 | -0.1903 | 0.3622 | 0.285 | -0.721 | 0.1926 | 0.8367 | 0.1382 | 0.5681 | 1.3364 | 0.1907 | 1.2128 | 118.7444 | 77.1163 | 72.5561 | 35 | 1.9042 | 0.4107 | -0.7053 | 0.6443 | 0.4437 | 1.1969 | -0.0709 | -0.0555 | -0.0252 | 0.1059 | -0.1355 | 0.2305 | 0.061 | -0.3347 | 0.167 | 0.5608 | 0.2728 | 0.322 | 0.8582 | 0.1496 | 0.7592 | 125.7325 | 81.1363 | 63.7806 | 36 | 4.9573 | 0.8903 | -1.0222 | 1.5207 | 1.116 | 1.5539 | 0.2726 | 0.3926 | 0.3582 | -0.1785 | -0.3485 | 0.4418 | -0.1649 | -0.1683 | 0.0657 | 0.8509 | 0.4827 | 0.2714 | 0.9727 | 0.0264 | 0.8398 | 121.681 | 95.4379 | 63.5896 | 37 | 0.5335 | 0.0762 | 0.6825 | 0.0106 | 0.098 | 0.8727 | -0.0234 | -0.0142 | -0.306 | 0.0207 | -0.0957 | 0.5833 | -0.0708 | -0.3831 | 0.1254 | 0.4884 | 0.369 | 0.0977 | 1.3253 | 0.0804 | 1.3076 | 106.2896 | 84.9104 | 49.5873 | 38 | 3.4033 | -2.1425 | 1.3726 | 1.8845 | -0.3066 | 1.1324 | -0.0403 | 0.6786 | 0.436 | -0.1779 | -0.2088 | 0.5475 | -0.2558 | -0.404 | 0.2729 | 0.2966 | 0.0885 | 0.0469 | 1.0317 | 0.1398 | 0.9875 | 120.4868 | 74.4955 | 44.903 | 39 | 1.2143 | 0.0305 | -0.1742 | 0.5493 | 0.2598 | 0.152 | -0.0248 | 0.1109 | 0.049 | 0.0265 | -0.0362 | 0.2747 | -0.0702 | -0.2491 | 0.0621 | 0.2031 | 0.2143 | 0.1095 | 0.5957 | 0.0887 | 0.4415 | 134.4435 | 79.1338 | 50.4703 | 40 | 2.736 | 0.2991 | -1.0376 | 1.2261 | -0.1386 | 1.3766 | 0.211 | 0.3455 | 0.2231 | -0.0321 | 0.0356 | 0.4481 | -0.1981 | -0.1825 | -0.2361 | 0.3434 | 0.1938 | 0.2053 | 0.7974 | 0.044 | 0.768 | 122.0465 | 78.2232 | 52.4474 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | (chain A and resid 1:8)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 9:59)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 60:66)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 67:73)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 74:93)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 94:99)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 104:123)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 124:130)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 131:145)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 146:155)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 156:173)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 174:182)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 183:188)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 189:205)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 206:233)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 234:257)17 | X-RAY DIFFRACTION | 17 | (chain A and resid 258:289)18 | X-RAY DIFFRACTION | 18 | (chain A and | | | | | | | | | | | | | | | | | |
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