Software | Name | Version | Classification |
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ADSC | Quantumdata collectionPHASER | | phasingPHENIX | (phenix.refine: 1.7.3_928)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.354→40.388 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 34.72 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2898 | 900 | 4.93 % | Random |
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Rwork | 0.2366 | - | - | - |
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all | 0.2394 | 18266 | - | - |
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obs | 0.2394 | 18266 | 57.86 % | - |
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.735 Å2 / ksol: 0.338 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.0482 Å2 | 0 Å2 | 7.3734 Å2 |
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2- | - | -2.0557 Å2 | -0 Å2 |
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3- | - | - | -19.5753 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.354→40.388 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2532 | 651 | 0 | 204 | 3387 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 3412 | X-RAY DIFFRACTION | f_angle_d0.709 | 4772 | X-RAY DIFFRACTION | f_dihedral_angle_d18.189 | 1264 | X-RAY DIFFRACTION | f_chiral_restr0.045 | 523 | X-RAY DIFFRACTION | f_plane_restr0.003 | 496 | | | | | |
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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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2.354-2.5017 | 0.6123 | 38 | 0.3951 | 826 | X-RAY DIFFRACTION | 17 | 2.5017-2.6948 | 0.399 | 90 | 0.3311 | 1657 | X-RAY DIFFRACTION | 33 | 2.6948-2.9659 | 0.299 | 123 | 0.3215 | 2386 | X-RAY DIFFRACTION | 48 | 2.9659-3.3949 | 0.3424 | 158 | 0.2655 | 3239 | X-RAY DIFFRACTION | 64 | 3.3949-4.2765 | 0.2688 | 234 | 0.2098 | 4367 | X-RAY DIFFRACTION | 87 | 4.2765-40.388 | 0.2595 | 257 | 0.213 | 4891 | 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 | 4.182 | -4.3367 | -1.0471 | 5.7002 | -0.164 | 1.5618 | -0.1166 | -0.0583 | 0.2005 | 0.0457 | -0.0113 | -0.3661 | -0.0927 | 0.0114 | 0.0336 | 0.1942 | 0.0759 | 0.0753 | 0.1921 | 0.0077 | 0.7461 | 33.9722 | -31.1707 | 0.7396 | 2 | 0.3496 | -0.3971 | 0.0741 | 0.5261 | -0.1479 | 0.1773 | -0.1142 | -0.0766 | -0.0493 | 0.0976 | -0.0123 | -0.1367 | 0.0024 | 0.0361 | -0.38 | -0.1551 | 0.2985 | -0.1357 | -0.3142 | 0.2164 | 0.4739 | 21.2899 | -33.5024 | 6.2763 | 3 | 0.4549 | -1.1866 | -0.2131 | 3.8521 | 0.504 | 0.3192 | -0.1233 | -0.1248 | -0.1826 | 0.3719 | 0.1895 | 0.0691 | 0.0731 | 0.018 | -0.0327 | 0.1014 | 0.0298 | -0.0018 | 0.0447 | 0.0176 | 0.3003 | 4.8656 | -14.2847 | 10.2045 | 4 | 0.0127 | -0.0392 | -0.0171 | 0.1479 | 0.0636 | 0.002 | 0.102 | 0.0092 | 0.2794 | -0.0594 | 0.1415 | -0.4024 | -0.0331 | 0.1845 | 0.8211 | -0.1866 | -0.2175 | 0.0116 | -0.844 | 0.0927 | 0.5273 | 20.2978 | 0.5977 | -3.065 | 5 | 0.9398 | -1.8592 | -1.3086 | 4.1273 | 1.7337 | 3.4561 | 0.0895 | -0.0371 | 0.1189 | 0.2531 | -0.2253 | 0.5751 | -0.5313 | -0.3004 | 0.2183 | 0.5122 | 0.0534 | -0.0911 | 0.2801 | -0.2717 | 0.7687 | 2.1103 | 14.9979 | 8.1837 | 6 | 1.271 | -1.7091 | 0.8939 | 8.0253 | -6.297 | 6.327 | 0.1253 | 0.0416 | 0.3025 | -0.8344 | -0.4473 | -2.2914 | -0.5158 | 0.3155 | 0.3258 | 0.4332 | 0.0433 | -0.1037 | 0.2122 | -0.0567 | 0.8382 | 10.0392 | -15.545 | -5.0237 | 7 | 3.3477 | 0.008 | -0.8665 | 0.1226 | -0.1275 | 0.3527 | 0.0248 | -0.2973 | 0.3558 | 0.0166 | -0.28 | 0.31 | -0.0433 | -0.4178 | 0.2536 | 0.5047 | -0.0869 | -0.344 | 0.5387 | -0.0703 | 1.2129 | 6.5804 | -18.371 | -5.7662 | 8 | 6.4829 | -1.7778 | -0.7146 | 0.5083 | 0.1039 | 0.4867 | 0.0339 | -0.2726 | -0.414 | -0.0001 | 0.0191 | 0.1027 | 0.1163 | -0.1584 | -0.049 | 0.436 | -0.0791 | -0.1952 | 0.6806 | 0.1335 | 1.5375 | 2.8556 | -21.7916 | -2.9764 | 9 | 7.2894 | 1.3013 | -0.0934 | 1.9259 | 0.5984 | 0.8354 | 0.1844 | -0.1081 | -0.6387 | 0.0447 | -0.0779 | 0.1191 | 0.2858 | -0.4227 | -0.1516 | 0.4951 | -0.156 | -0.3965 | 0.946 | 0.1529 | 1.0623 | 6.0389 | -24.1003 | 0.5917 | 10 | 6.7597 | -0.586 | 1.6278 | 6.0726 | 1.862 | 3.4905 | 0.3491 | -0.3078 | -0.8833 | 0.0907 | -0.1932 | 0.2707 | 0.423 | -0.1463 | -0.1873 | 0.3023 | -0.075 | -0.2565 | 0.3555 | 0.0043 | 0.8149 | 10.5844 | -24.1128 | 1.7638 | 11 | 2.1598 | 0.009 | 0.3768 | 1.479 | 1.2884 | 1.1852 | -0.0024 | 0.0027 | 0.0039 | -0.0558 | 0.0369 | -0.2754 | -0.0208 | 0.0488 | -0.0755 | 0.1994 | -0.0842 | -0.0598 | 0.2385 | 0.075 | 0.627 | 15.2377 | -22.1419 | 0.4143 | 12 | 1.0577 | -0.2205 | -0.2428 | 0.5012 | 0.52 | 0.8428 | 0.0378 | 0.0968 | -0.1449 | 0.0147 | 0.0848 | -0.1603 | 0.077 | 0.1344 | -0.1183 | 0.1897 | 0.046 | -0.1662 | 0.2054 | -0.1878 | 0.5181 | 18.5844 | -18.2142 | -0.3099 | 13 | 3.4458 | 1.9924 | 0.7913 | 1.8776 | 0.7233 | 2.2319 | 0.1381 | -0.4101 | 0.3585 | 0.0318 | -0.2511 | 0.3286 | -0.0039 | -0.1649 | 0.1169 | 0.2742 | -0.093 | -0.1971 | 0.2897 | 0.1258 | 0.7486 | 21.068 | -14.2505 | 0.3892 | 14 | 2.6982 | 2.0515 | 1.7933 | 2.2746 | 1.3107 | 3.385 | 0.0932 | -0.0145 | -0.2719 | 0.0435 | -0.0007 | -0.1543 | 0.0903 | 0.0852 | -0.0807 | 0.2011 | -0.0288 | -0.137 | 0.217 | -0.0967 | 0.4665 | 22.2161 | -10.5308 | 4.1861 | 15 | 6.397 | 2.6317 | 1.7605 | 3.1699 | 0.1847 | 2.8128 | 0.108 | -0.0196 | -0.2631 | 0.0345 | -0.0146 | -0.0911 | 0.0935 | 0.0715 | -0.0767 | 0.2805 | -0.0904 | -0.1748 | 0.3288 | -0.1129 | 0.5778 | 22.822 | -9.8237 | 9.7023 | 16 | 7.1635 | 0.8686 | 3.0308 | 1.215 | 0.5747 | 4.9447 | 0.0012 | -0.1424 | 0.0431 | 0.035 | 0.0489 | -0.0755 | 0.0373 | -0.1638 | -0.0112 | 0.3991 | 0.0475 | -0.3198 | 0.3897 | -0.1252 | 0.9556 | 24.3653 | -10.0779 | 14.4525 | 17 | 0.7655 | 0.6317 | 0.1941 | 0.5486 | 0.203 | 0.6301 | -0.025 | -0.0989 | 0.2611 | -0.0643 | -0.0253 | 0.2095 | 0.0018 | -0.2241 | 0.0788 | 0.5287 | -0.1274 | -0.3473 | 0.7006 | -0.1479 | 0.9221 | 26.8245 | -12.2693 | 18.5475 | 18 | 4.8598 | 3.4394 | -4.6357 | 7.7517 | -1.6771 | 4.9056 | -0.0221 | -1.4773 | 0.5168 | -0.4289 | 0.2468 | 1.0802 | 0.0904 | -1.899 | -0.2552 | 0.4903 | 0.0484 | -0.4049 | 0.8498 | -0.0416 | 0.7199 | 29.5464 | -16.2065 | 21.1804 | 19 | 8.9879 | 1.4412 | -3.0751 | 8.1805 | -4.8744 | 7.6439 | 0.5659 | -0.2026 | -1.5743 | 0.0268 | -0.237 | -0.0895 | 0.9605 | 0.4404 | -0.3749 | 0.6407 | 0.1683 | -0.4559 | 0.9695 | 0.1658 | 0.9503 | 33.2153 | -19.5226 | 21.8288 | 20 | 2 | -4.7245 | 4.7853 | 6.8477 | -3.9559 | 9.9571 | 1.2439 | 0.1652 | -3.5861 | -0.5072 | -0.3905 | 0.7817 | 1.3352 | -0.546 | -0.8989 | 0.4912 | 0.1343 | -0.3562 | 0.8196 | 0.0593 | 1.1949 | 37.7935 | -21.0655 | 20.5482 | 21 | 7.3916 | -2.2892 | 3.8237 | 6.9561 | -1.024 | 9.3954 | 0.7304 | 0.3928 | -2.013 | -0.0818 | -0.1783 | 0.1038 | 0.9952 | -0.4288 | -0.6221 | 0.4714 | -0.0436 | -0.4048 | 0.8843 | -0.0443 | 0.9427 | 42.9781 | -20.6008 | 19.7696 | 22 | 2.2691 | -2.5839 | -3.3742 | 8.7529 | 3.6696 | 6.4056 | 0.3261 | 0.9587 | -1.243 | 0.0739 | 0.2238 | -0.646 | 0.447 | 1.1243 | -0.584 | 0.5476 | -0.0382 | -0.4748 | 1.1334 | -0.0696 | 1.0703 | 47.0934 | -18.343 | 19.7321 | 23 | 8.1517 | 0.7513 | -0.3586 | 8.9422 | -5.3162 | 4.309 | 0.6217 | 2.5908 | -2.2819 | -0.6682 | 0.5076 | 0.1251 | 1.7827 | 0.0322 | -1.1393 | 0.9031 | -0.0531 | -0.6417 | 1.4335 | -0.164 | 1.2838 | 49.7912 | -14.3964 | 20.9979 | 24 | 4.7074 | 0.8713 | -0.0029 | 3.5687 | 1.8726 | 2.6958 | -0.8949 | -0.4891 | 2.8712 | -0.1296 | 0.1393 | 0.5896 | -0.9413 | -0.2959 | 0.7826 | 0.8799 | 0.0171 | -0.6375 | 1.399 | -0.1527 | 1.4389 | 44.7198 | -11.8787 | 29.611 | 25 | 9.7565 | -6.9747 | 2.3418 | 7.9794 | -6.255 | 7.5728 | -0.8463 | -2.3315 | 2.7236 | 0.3856 | -0.4531 | 0.1991 | -1.3646 | -0.2489 | 1.3291 | 0.9361 | 0.0699 | -0.6717 | 1.6585 | -0.1382 | 1.5828 | 42.526 | -9.2908 | 26.8297 | 26 | 2 | 3.3733 | -8.4395 | 1.2333 | -1.9645 | 2 | -1.276 | -3.244 | 5.4329 | 0.2809 | -0.5247 | 1.0293 | -2.9855 | 0.6959 | 1.8157 | 0.9452 | -0.042 | -0.6496 | 1.2457 | -0.2501 | 1.6088 | 41.9615 | -8.6592 | 22.0593 | 27 | 2.7313 | 4.9543 | -0.6799 | 8.9867 | -1.2468 | 8.4842 | -0.7999 | -1.272 | 4.4598 | -0.2812 | -0.2615 | 1.0464 | -1.6666 | 0.4374 | 1.0885 | 0.6573 | -0.0665 | -0.4966 | 0.7899 | -0.0198 | 1.4592 | 40.8075 | -9.7631 | 17.6791 | 28 | 9.1971 | -5.6881 | 1.2407 | 4.581 | 1.4726 | 4.8866 | -0.7387 | 1.0494 | 2.4704 | 0.4437 | 0.4156 | -0.9894 | -0.7975 | 1.1782 | 0.3369 | 0.6135 | -0.0395 | -0.4805 | 0.5938 | -0.0096 | 1.0655 | 39.687 | -12.8518 | 14.0151 | 29 | 5.9031 | -6.6231 | 1.2312 | 8.6336 | 1.5012 | 7.1641 | 0.0955 | 1.2355 | 0.912 | 0.5864 | 0.1504 | -1.6387 | 0.3197 | 1.6583 | -0.2659 | 0.4191 | 0.0344 | -0.3489 | 0.7202 | -0.0279 | 0.9279 | 37.0873 | -16.1816 | 11.8619 | 30 | 1.0327 | -1.1703 | -0.4138 | 1.7857 | 0.2698 | 0.2522 | 0.1253 | 0.1256 | -0.2897 | 0.1257 | 0.0458 | -0.3796 | 0.1946 | 0.1096 | -0.1919 | 0.3492 | -0.0313 | -0.2986 | 0.5844 | -0.0928 | 0.9013 | 32.9176 | -19.0063 | 11.144 | 31 | 6.3762 | 0.012 | 2.7226 | 1.6826 | -0.0306 | 3.3049 | -0.2017 | -0.1968 | 0.6987 | -0.0196 | 0.0544 | 0.0556 | -0.2695 | -0.0174 | 0.127 | 0.3816 | 0.0362 | -0.3024 | 0.4325 | 0.0178 | 1.0499 | 28.5012 | -20.9415 | 13.1993 | 32 | 8.1904 | 1.6881 | 0.9424 | 1.8912 | -0.1849 | 3.3799 | 0.2655 | -0.3791 | -1.0746 | 0.0633 | 0.0119 | -0.1885 | 0.3813 | 0.0072 | -0.2901 | 0.3137 | -0.0196 | -0.2086 | 0.5031 | -0.0149 | 1.1024 | 24.4556 | -20.4373 | 15.2062 | 33 | 4.7209 | 1.826 | 1.3791 | 1.4505 | 1.0529 | 3.2677 | 0.2201 | -0.2781 | -0.5048 | 0.1624 | -0.0516 | -0.1334 | 0.2974 | -0.0565 | -0.1866 | 0.3033 | -0.0965 | -0.269 | 0.4445 | 0.0235 | 0.5521 | 20.2939 | -17.4352 | 14.0227 | 34 | 5.993 | -2.4455 | -3.359 | 0.9997 | 1.3035 | 4.2759 | -0.0836 | -0.9239 | -0.767 | 0.0762 | -0.1347 | 0.4951 | 0.2061 | 0.0076 | 0.2321 | 0.1749 | -0.0662 | -0.0672 | 0.3982 | 0.175 | 0.7069 | 16.7322 | -14.6426 | 11.8484 | 35 | 3.3086 | 0.3348 | 0.8961 | 0.2593 | 0.4822 | 1.0403 | -0.0269 | -0.0555 | 0.2169 | -0.0066 | -0.0098 | 0.0069 | -0.0423 | -0.049 | 0.0794 | 0.2094 | -0.0848 | -0.1621 | 0.278 | 0.1975 | 0.5345 | 14.2372 | -11.9884 | 8.6102 | 36 | 8.0649 | 0.9817 | 3.3879 | 3.7339 | -0.2633 | 4.0002 | -0.1316 | -0.2548 | 0.287 | 0.099 | 0.0858 | -0.0435 | -0.1328 | -0.1297 | 0.0679 | 0.3255 | 0.1211 | -0.258 | 0.2748 | -0.1546 | 0.4905 | 12.9178 | -11.0391 | 3.5858 | 37 | 0.1232 | 0.0533 | -0.0489 | 0.0593 | 0.0169 | 0.0592 | -0.0012 | -0.0055 | -0.0181 | 0.0003 | 0.0077 | 0.0186 | 0.0039 | -0.0117 | -0.0179 | 0.162 | 0.0083 | -0.1494 | 0.3824 | 0.0073 | 0.2854 | 11.3474 | -13.4271 | -1.0873 |
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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 103:1222 | X-RAY DIFFRACTION | 2 | chain A and resid 124:1953 | X-RAY DIFFRACTION | 3 | chain A and resid 197:2194 | X-RAY DIFFRACTION | 4 | chain A and resid 220:4095 | X-RAY DIFFRACTION | 5 | chain A and resid 410:4216 | X-RAY DIFFRACTION | 6 | chain C and resid 15:157 | X-RAY DIFFRACTION | 7 | chain C and resid 16:168 | X-RAY DIFFRACTION | 8 | chain C and resid 17:179 | X-RAY DIFFRACTION | 9 | chain C and resid 18:1810 | X-RAY DIFFRACTION | 10 | chain C and resid 19:1911 | X-RAY DIFFRACTION | 11 | chain C and resid 20:2012 | X-RAY DIFFRACTION | 12 | chain C and resid 21:2113 | X-RAY DIFFRACTION | 13 | chain C and resid 22:2214 | X-RAY DIFFRACTION | 14 | chain C and resid 23:2315 | X-RAY DIFFRACTION | 15 | chain C and resid 24:2416 | X-RAY DIFFRACTION | 16 | chain C and resid 25:2517 | X-RAY DIFFRACTION | 17 | chain C and resid 26:2618 | X-RAY DIFFRACTION | 18 | chain C and | | | | | | | | | | | | | | | | | |
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