Software | Name | Version | Classification | NB |
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SCALA | 3.3.20data scaling | PHENIX | 1.8.2_1309refinement | PDB_EXTRACT | 3.11 | data extraction | MAR345dtb | | data collection | MOSFLM | | data reduction | PHASER | | phasing | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30.01 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8045 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.241 | 5227 | 5.03 % | Random |
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Rwork | 0.1923 | - | - | - |
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all | 0.1947 | 104402 | - | - |
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obs | 0.1947 | 103947 | 91.04 % | - |
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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: 125.28 Å2 / Biso mean: 30.4438 Å2 / Biso min: 7.52 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.1→30.01 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 13062 | 0 | 60 | 634 | 13756 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 13382 | X-RAY DIFFRACTION | f_angle_d1.078 | 18152 | X-RAY DIFFRACTION | f_chiral_restr0.066 | 2098 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2324 | X-RAY DIFFRACTION | f_dihedral_angle_d13.262 | 4825 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.1-2.1239 | 0.2917 | 197 | 0.2255 | 3605 | 3802 | 100 | 2.1239-2.1489 | 0.2548 | 189 | 0.2187 | 3601 | 3790 | 100 | 2.1489-2.1751 | 0.27 | 176 | 0.2056 | 3580 | 3756 | 100 | 2.1751-2.2026 | 0.2732 | 196 | 0.2195 | 3559 | 3755 | 100 | 2.2026-2.2315 | 0.347 | 168 | 0.2621 | 3570 | 3738 | 98 | 2.2315-2.2621 | 0.4815 | 18 | 0.3145 | 388 | 406 | 97 | 2.2621-2.2944 | 0.3409 | 145 | 0.2633 | 3167 | 3312 | 96 | 2.2944-2.3286 | 0.2838 | 207 | 0.2082 | 3570 | 3777 | 100 | 2.3286-2.365 | 0.2848 | 188 | 0.1971 | 3611 | 3799 | 100 | 2.365-2.4038 | 0.2493 | 208 | 0.2045 | 3545 | 3753 | 100 | 2.4038-2.4452 | 0.2508 | 194 | 0.2014 | 3586 | 3780 | 100 | 2.4452-2.4897 | 0.3009 | 192 | 0.2118 | 3604 | 3796 | 100 | 2.4897-2.5375 | 0.27 | 189 | 0.2078 | 3645 | 3834 | 100 | 2.5375-2.5893 | 0.2564 | 216 | 0.2014 | 3538 | 3754 | 100 | 2.5893-2.6456 | 0.2967 | 195 | 0.2177 | 3605 | 3800 | 100 | 2.6456-2.7071 | 0.3096 | 70 | 0.2274 | 1201 | 1271 | 34 | 2.7071-2.7747 | 0.2385 | 179 | 0.2028 | 3566 | 3745 | 99 | 2.7747-2.8497 | 0.279 | 183 | 0.1953 | 3615 | 3798 | 100 | 2.8497-2.9335 | 0.2585 | 181 | 0.213 | 3594 | 3775 | 100 | 2.9335-3.0281 | 0.2903 | 190 | 0.2165 | 3639 | 3829 | 100 | 3.0281-3.1362 | 0.2642 | 190 | 0.2105 | 3614 | 3804 | 100 | 3.1362-3.2616 | 0.2509 | 204 | 0.2101 | 3577 | 3781 | 100 | 3.2616-3.4098 | 0.2567 | 181 | 0.2033 | 3626 | 3807 | 100 | 3.4098-3.5893 | 0.2649 | 124 | 0.2012 | 2529 | 2653 | 70 | 3.5893-3.8138 | 0.2062 | 127 | 0.1831 | 2448 | 2575 | 68 | 3.8138-4.1076 | 0.1981 | 130 | 0.1625 | 2603 | 2733 | 71 | 4.1076-4.5197 | 0.1745 | 198 | 0.1401 | 3611 | 3809 | 100 | 4.5197-5.1708 | 0.1689 | 176 | 0.1425 | 3659 | 3835 | 100 | 5.1708-6.5038 | 0.1863 | 217 | 0.1655 | 3639 | 3856 | 100 | 6.5038-30.0132 | 0.2132 | 199 | 0.1791 | 3625 | 3824 | 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 | 2.0184 | 0.2908 | -0.5271 | 3.2733 | 1.6835 | 1.8135 | 0.3675 | 0.5762 | 0.3658 | -0.8801 | -0.3176 | -0.2055 | -0.2579 | 0.2128 | -0.0564 | 0.2605 | 0.0634 | 0.0841 | 0.3008 | 0.0413 | 0.4802 | 15.0572 | -22.9714 | -74.4023 | 2 | 1.3873 | -0.4076 | -0.3663 | 0.9209 | -0.2344 | 1.4454 | -0.0842 | 0.1164 | -0.0302 | -0.1478 | 0.0201 | -0.3005 | 0.1792 | 0.2311 | -0.0073 | 0.2118 | 0.0553 | 0.0914 | 0.1245 | -0.0525 | 0.3352 | 12.13 | -29.4813 | -71.7923 | 3 | 2.2588 | -0.9298 | 0.4112 | 2.0466 | 0.0398 | 0.9534 | 0.1269 | 0.1549 | -0.3145 | -0.1473 | -0.1284 | -0.1427 | 0.1251 | 0.0447 | 0.006 | 0.1279 | 0.0296 | 0.0118 | 0.0914 | -0.0133 | 0.1871 | 5.8466 | -23.9129 | -67.5968 | 4 | 1.3419 | 0.3063 | -0.3187 | 1.7753 | -0.4141 | 1.719 | -0.0029 | -0.1171 | -0.0954 | 0.0653 | -0.0653 | -0.0284 | 0.0627 | 0.0278 | 0.049 | 0.1058 | -0.0416 | -0.0165 | 0.0892 | 0.0019 | 0.1599 | 3.0837 | -17.8275 | -56.75 | 5 | 1.392 | 0.0752 | -0.1061 | 0.8685 | 0.0969 | 0.9315 | 0.076 | -0.0768 | 0.1388 | 0.1256 | -0.0623 | -0.1575 | -0.2579 | 0.1597 | -0.013 | 0.152 | -0.0578 | -0.0135 | 0.1106 | 0.0012 | 0.1427 | 8.1483 | -7.8747 | -60.9789 | 6 | 5.0087 | 0.796 | -2.2821 | 6.0392 | 3.3273 | 3.3437 | -0.0729 | 0.4429 | 0.9297 | -0.3445 | -0.0482 | 0.4752 | -1.1152 | -0.3175 | 0.155 | 0.3797 | 0.0777 | -0.0123 | 0.1832 | 0.0306 | 0.2927 | -4.5127 | 1.7573 | -69.4431 | 7 | 2.5646 | 0.1186 | -0.6013 | 1.3299 | 0.0687 | 1.299 | 0.0055 | -0.0274 | -0.168 | -0.0217 | -0.1227 | -0.4384 | 0.098 | 0.3973 | 0.1103 | 0.126 | -0.0069 | -0.0288 | 0.1264 | -0.0565 | 0.2062 | 14.8043 | -18.4806 | -62.7399 | 8 | 2 | -7.25 | 2 | 2 | -0.7818 | 2 | -0.0883 | 0.0552 | -0.036 | -0.0138 | 0.0065 | 0.0684 | 0.0724 | -0.0523 | 0.0639 | 0.1462 | -0.0452 | -0.0573 | 0.1999 | -0.1546 | 0.1887 | -1.3212 | -8.1826 | -68.1467 | 9 | 0.8915 | -0.0501 | 0.1019 | 6.5208 | -2.0601 | 5.8767 | -0.1751 | -0.4185 | -0.6299 | 0.2236 | -0.071 | -0.2417 | 0.354 | 0.2534 | 0.243 | 0.2724 | -0.0211 | 0.0839 | 0.1865 | -0.0038 | 0.2457 | -15.1159 | -35.8924 | -29.4867 | 10 | 0.6557 | 0.0408 | -0.5962 | 0.5489 | -0.3447 | 0.8609 | -0.1419 | 0.0123 | -0.3403 | 0.039 | -0.0452 | 0.0431 | 0.3285 | -0.1231 | 0.149 | 0.3051 | -0.1346 | 0.0421 | 0.2198 | -0.0203 | 0.2789 | -16.0336 | -35.2186 | -38.0694 | 11 | 1.663 | -0.5794 | -0.7348 | 1.1048 | -0.707 | 1.4027 | -0.0057 | -0.0525 | 0.0909 | 0.2119 | -0.0657 | 0.0254 | -0.2522 | -0.0894 | 0.0474 | 0.269 | -0.0892 | 0.0214 | 0.15 | -0.0183 | 0.1619 | -14.0403 | -17.0692 | -34.6123 | 12 | 0.391 | -0.2265 | -0.7668 | 1.7165 | -0.4021 | 1.9469 | 0.0927 | -0.1944 | -0.0514 | 0.237 | -0.1424 | -0.1246 | -0.0801 | 0.1408 | 0.0334 | 0.2013 | -0.0806 | -0.0254 | 0.1673 | 0.0113 | 0.1429 | -5.2819 | -17.5795 | -41.0832 | 13 | 0.9211 | 0.3428 | -1.2706 | 1.5436 | -0.7542 | 3.166 | -0.0235 | -0.4369 | -0.2993 | 0.2722 | -0.0916 | 0.1605 | 0.0157 | -0.1177 | 0.09 | 0.3089 | -0.1013 | 0.071 | 0.1052 | -0.057 | 0.2219 | -17.3155 | -25.6358 | -30.6496 | 14 | 8.7125 | 4.438 | 5.1486 | 8.2514 | -3.4292 | 9.156 | 0.0956 | 0.3431 | 0.6697 | -0.1773 | 0.2833 | 0.5199 | 0.4294 | -0.1085 | -0.3697 | 0.2471 | -0.0218 | 0.0454 | 0.5138 | -0.0136 | 0.3144 | -1.1948 | -20.8085 | -40.496 | 15 | 0.693 | -0.3206 | -0.0323 | 0.8955 | -0.3444 | 0.1755 | 0.1293 | 0.2717 | -0.3028 | -0.176 | 0.0551 | 0.5958 | 0.1186 | -0.5699 | -0.2679 | 0.101 | 0.1709 | -0.2055 | 0.923 | -0.2269 | 0.4743 | -38.4027 | -12.7287 | -72.9495 | 16 | 0.4198 | -0.1809 | 0.5719 | 0.6772 | 0.2499 | 1.2719 | 0.0896 | 0.4136 | -0.2609 | -0.0878 | -0.3269 | 0.4926 | 0.1787 | -0.8385 | -0.1502 | 0.1869 | 0.0408 | -0.0651 | 0.5705 | -0.1962 | 0.3057 | -30.7153 | -17.0061 | -71.3483 | 17 | 2.2571 | -0.6112 | -1.1234 | 1.0052 | 0.3429 | 1.9766 | 0.1376 | 0.1529 | -0.1087 | 0.0295 | -0.1751 | 0.0406 | -0.0482 | -0.3808 | 0 | 0.1128 | 0.0323 | -0.0515 | 0.1884 | -0.0357 | 0.1369 | -17.9597 | -9.9625 | -64.7341 | 18 | 0.8826 | -0.1066 | -0.1084 | 0.4694 | 0.0176 | 0.708 | 0.1587 | 0.2259 | 0.1034 | -0.0278 | -0.1455 | 0.1296 | -0.2956 | -0.3209 | -0.0338 | 0.2346 | 0.1157 | 0.0024 | 0.3064 | -0.0264 | 0.1799 | -24.797 | -1.2785 | -60.0874 | 19 | 2.0531 | -0.3219 | -0.9972 | 1.6626 | 0.6564 | 1.8612 | 0.2581 | 0.3957 | -0.0662 | 0.0845 | -0.26 | 0.1226 | 0.2071 | 0.0455 | -0.054 | 0.1199 | 0.2531 | -0.0365 | 0.4854 | -0.1189 | 0.2975 | -39.7833 | -2.8775 | -61.8175 | 20 | 4.2166 | -2.417 | 1.1925 | 1.3894 | -0.6846 | 0.3342 | 0.1863 | 0.5229 | 0.1001 | -0.3229 | -0.1295 | 0.0844 | -0.359 | -0.2973 | -0.0044 | 0.3906 | 0.2858 | -0.0541 | 0.6307 | 0.0505 | 0.1709 | -19.8083 | -3.8841 | -83.0085 | 21 | 8.3892 | -1.5846 | 4.6968 | 3.1036 | 2.0534 | 5.7113 | 0.0954 | 0.9363 | -0.0302 | -1.0754 | 0.2906 | -0.7034 | -0.2898 | 0.8547 | -0.2908 | 0.3362 | 0.0454 | 0.0665 | 0.2785 | -0.0172 | 0.2282 | -4.219 | -15.1707 | -81.5371 | 22 | 2.3706 | 0.6755 | 0.6044 | 2.7729 | 0.9297 | 3.1249 | 0.0895 | -0.3201 | -0.1855 | 0.2439 | -0.0166 | -0.3751 | 0.0959 | 0.4616 | -0.0871 | 0.1637 | -0.0063 | -0.0279 | 0.2373 | 0.0446 | 0.2209 | 47.4664 | -58.158 | -0.5023 | 23 | 1.0655 | -0.3345 | -0.0839 | 0.4193 | 0.4648 | 1.0476 | 0.0741 | -0.0061 | 0.0596 | -0.0324 | -0.0095 | -0.0945 | -0.2052 | 0.0657 | -0.0285 | 0.2447 | -0.0509 | 0.0127 | 0.1177 | 0.002 | 0.192 | 37.3515 | -44.9313 | -10.6809 | 24 | 2.8527 | 0.2264 | 0.3495 | 2.3051 | -0.601 | 0.2247 | 0.0379 | 0.1204 | -0.0973 | -0.2151 | -0.0488 | -0.1406 | -0.2519 | 0.2306 | 0.0186 | 0.2228 | -0.0481 | 0.0339 | 0.1172 | -0.0118 | 0.1698 | 38.8864 | -48.9724 | -10.3917 | 25 | 2.0378 | 0.0862 | -0.55 | 1.1367 | 0.1887 | 1.9419 | 0.0034 | -0.2899 | 0.0531 | 0.0742 | 0.0407 | -0.0718 | -0.0915 | 0.1605 | -0.0523 | 0.2968 | -0.0627 | -0.0168 | 0.1035 | 0.025 | 0.1989 | 39.119 | -46.7672 | 0.6651 | 26 | 2.0716 | 0.8 | -0.1258 | 2.0566 | -0.8856 | 1.1104 | 0.0421 | -0.1014 | -0.2525 | 0.3715 | -0.11 | 0.3344 | 0.1177 | -0.3062 | 0.0864 | 0.2933 | -0.0634 | 0.0971 | 0.3072 | -0.0057 | 0.3429 | 2.987 | -64.9534 | -3.4395 | 27 | 1.9376 | -0.3073 | -0.3317 | 1.8031 | 0.8438 | 1.6244 | -0.0636 | 0.1737 | 0.0687 | -0.1019 | -0.0463 | 0.1338 | -0.1751 | -0.2852 | 0.1098 | 0.2304 | 0.0632 | 0.0115 | 0.2425 | 0.0148 | 0.1703 | 5.644 | -50.7833 | -14.9454 | 28 | 2.2643 | 0.6985 | 0.0179 | 1.3994 | 0.2558 | 1.5073 | 0.0382 | -0.04 | 0.0897 | -0.0025 | -0.0668 | 0.2326 | -0.1415 | -0.3178 | 0.0392 | 0.2039 | 0.0659 | 0.031 | 0.2131 | 0.0094 | 0.2054 | 7.9056 | -52.7012 | -10.678 | 29 | 5.6263 | 2.9171 | 1.4296 | 4.8771 | 3.4865 | 4.0068 | -0.7108 | 0.5782 | -0.3038 | 0.5511 | 0.3363 | -0.3368 | 0.7757 | -0.8137 | 0.356 | 0.3153 | 0.0551 | 0.0303 | 0.3773 | 0.0606 | 0.15 | 15.7753 | -48.1277 | -4.7646 | 30 | 0.7482 | -0.275 | -1.28 | 2.1839 | 0.6462 | 4.5533 | 0.0281 | 0.3449 | -0.2033 | -0.0741 | -0.2568 | 0.0177 | 0.6797 | -0.2393 | 0.206 | 0.2839 | 0.0245 | 0.0068 | 0.235 | -0.067 | 0.2377 | 30.5199 | -78.7486 | -40.1439 | 31 | 1.6265 | -0.1731 | -0.0639 | 1.0262 | 0.7242 | 1.4871 | 0.1111 | 0.1553 | 0.0048 | -0.1455 | -0.1342 | 0.035 | -0.2601 | -0.2024 | 0.0237 | 0.2193 | 0.0731 | 0.013 | 0.1719 | -0.0037 | 0.1324 | 29.2145 | -62.0169 | -36.2902 | 32 | 0.428 | -0.0083 | -0.4438 | 2.1591 | 0.2415 | 1.4796 | 0.11 | 0.2762 | -0.0279 | -0.16 | -0.2308 | 0.3705 | -0.2894 | -0.4852 | 0.0893 | 0.2388 | 0.1003 | -0.01 | 0.296 | -0.0453 | 0.1798 | 19.884 | -57.5952 | -32.024 | 33 | 1.9655 | 0.1466 | -0.3884 | 1.4148 | 0.7193 | 2.9811 | 0.0645 | 0.5532 | -0.2519 | -0.1972 | -0.076 | -0.065 | -0.0617 | -0.0296 | 0.0171 | 0.2284 | 0.0895 | 0.0334 | 0.1284 | 0.0062 | 0.1729 | 32.2509 | -66.1698 | -41.9683 | 34 | 4.1031 | 1.9575 | 2.9709 | 8.7241 | 3.8518 | 2.9119 | -0.0326 | -0.3236 | 0.3016 | 0.3666 | 0.379 | -0.8294 | 0.7012 | 0.0774 | -0.3352 | 0.3644 | 0.0658 | -0.0369 | 0.3512 | -0.1435 | 0.1635 | 15.9387 | -60.7209 | -32.7366 |
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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 3 through 26 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 27 through 53 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 54 through 90 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 91 through 139 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 140 through 230 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 231 through 242 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 243 through 291 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 301 through 301 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 1 through 23 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 24 through 90 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 91 through 182 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 183 through 242 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 243 through 290 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 301 through 301 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 3 through 26 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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