Software | Name | Version | Classification |
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CrystalClear | | data 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: 2.5→37.77 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 32.06 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.278 | 946 | 5.04 % |
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Rwork | 0.225 | - | - |
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obs | 0.225 | 18780 | 72.3 % |
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all | - | 18780 | - |
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.74 Å2 / ksol: 0.33 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.5253 Å2 | -0 Å2 | 3.2065 Å2 |
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2- | - | -4.6631 Å2 | -0 Å2 |
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3- | - | - | -15.5525 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.5→37.77 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2527 | 649 | 0 | 151 | 3327 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 3364 | X-RAY DIFFRACTION | f_angle_d0.73 | 4698 | X-RAY DIFFRACTION | f_dihedral_angle_d20.057 | 1293 | X-RAY DIFFRACTION | f_chiral_restr0.043 | 516 | X-RAY DIFFRACTION | f_plane_restr0.003 | 486 | | | | | |
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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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2.5-2.633 | 0.3098 | 22 | 0.3455 | 476 | X-RAY DIFFRACTION | 13 | 2.633-2.7979 | 0.3922 | 73 | 0.3239 | 1362 | X-RAY DIFFRACTION | 39 | 2.7979-3.0139 | 0.4196 | 130 | 0.3195 | 2369 | X-RAY DIFFRACTION | 68 | 3.0139-3.317 | 0.3519 | 146 | 0.2895 | 3203 | X-RAY DIFFRACTION | 90 | 3.317-3.7966 | 0.2865 | 195 | 0.2235 | 3429 | X-RAY DIFFRACTION | 98 | 3.7966-4.7818 | 0.2278 | 200 | 0.1753 | 3457 | X-RAY DIFFRACTION | 98 | 4.7818-37.767 | 0.2238 | 180 | 0.1914 | 3538 | 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 | 2.9939 | -0.717 | 0.5246 | 6.6283 | 2.3626 | 6.2866 | 0.2979 | 0.1285 | -0.2664 | 0.0515 | -0.0184 | -0.16 | 0.1105 | 0.3987 | -0.3058 | 0.2656 | 0.0595 | 0.0972 | 0.2624 | -0.0313 | 0.9108 | 33.7106 | -30.5919 | 0.9495 | 2 | 1.0346 | -0.6498 | -0.1308 | 1.6168 | -0.0537 | 0.61 | -0.1931 | -0.1223 | -0.6362 | 0.2896 | 0.0023 | -0.3445 | 0.1312 | 0.0429 | -0.2 | 0.1438 | 0.1526 | -0.0636 | -0.0977 | 0.1153 | 0.721 | 21.2122 | -33.01 | 6.1334 | 3 | 1.2208 | 0.0425 | 0.3745 | 1.7974 | -0.0463 | 1.5838 | 0.1119 | -0.1731 | -0.197 | 0.2677 | 0.0804 | 0.0704 | 0.0682 | 0.1192 | 0.3769 | 0.0605 | 0.0772 | -0.0099 | 0.1822 | 0.1146 | -0.0237 | 4.7635 | -14.1939 | 10.2301 | 4 | 1.117 | -0.6703 | 0.2621 | 1.096 | 0.2261 | 0.2463 | -0.1457 | 0.3388 | 0.919 | -0.1956 | 0.0599 | -0.9095 | -0.2689 | 0.5529 | -0.0533 | -0.4244 | -0.5526 | 0.2203 | -1.014 | 0.1837 | 0.1308 | 20.2227 | 0.7177 | -2.9561 | 5 | -0.0001 | 0.0002 | -0.0003 | 0.0086 | -0.0128 | 0.0209 | 0.048 | -0.1657 | 0.3757 | 0.2155 | -0.2737 | 0.9976 | -0.1015 | -0.3587 | 0.2203 | 0.2421 | -0.0003 | 0.0586 | 0.2522 | -0.2415 | 0.9127 | 1.747 | 15.1069 | 8.3349 | 6 | 0.1137 | 0.5763 | 0.4705 | 6.1052 | 2.3627 | 1.9478 | 0.0253 | 0.0234 | 0.0132 | -0.5237 | 0.0326 | -0.3884 | 0.1158 | 0.2192 | 0.0039 | 0.2747 | 0.0113 | 0.0429 | 0.4306 | -0.2195 | 0.3095 | 10.133 | -15.2961 | -4.876 | 7 | 1.2643 | 0.3751 | 0.5655 | 2.0565 | 1.4407 | 1.086 | -0.1769 | -0.0228 | -0.1341 | 0.0308 | 0.0549 | 0.0646 | 0.2712 | -0.0262 | 0.1702 | 0.5081 | 0.0841 | 0.0844 | 0.4079 | -0.2246 | 0.3527 | 6.7043 | -18.3034 | -5.6429 | 8 | 1.7023 | 1.0432 | 1.6316 | 6.4336 | -4.7521 | 7.2734 | -0.1141 | 0.0158 | 0.1796 | 0.1629 | 0.1676 | 0.0999 | -0.1593 | -0.1608 | -0.0469 | 0.3877 | -0.1052 | -0.123 | 0.4994 | 0.0744 | 1.3068 | 3.0373 | -21.6795 | -3.2221 | 9 | 0.4933 | -0.3103 | -0.6138 | 1.894 | 1.0829 | 1.0495 | 0.1913 | -0.4177 | -0.3841 | 0.1348 | -0.2385 | 0.1927 | 0.1661 | -0.3053 | 0.0172 | 0.3755 | -0.1216 | -0.1111 | 0.9598 | 0.5089 | 0.8652 | 6.0179 | -24.0447 | 0.5033 | 10 | 3.1253 | -2.9368 | -0.5294 | 3.6642 | 0.9379 | 2.4317 | 0.1723 | 0.0327 | -0.36 | 0.1524 | -0.3813 | 0.6442 | 0.4558 | -0.3629 | 0.2163 | 0.4411 | -0.1794 | -0.1832 | 0.3842 | -0.0524 | 0.5421 | 10.7073 | -23.8989 | 1.609 | 11 | 1.2775 | 1.3721 | 1.3004 | 3.4799 | -0.2834 | 2.731 | 0.2369 | 0.104 | 0.0447 | -0.4419 | -0.1051 | 0.0725 | -0.1481 | -0.1592 | -0.0487 | 0.2267 | 0.0102 | 0.0407 | 0.114 | 0.0214 | 0.4586 | 15.2909 | -21.7673 | 0.3725 | 12 | 5.0395 | 1.3639 | 0.4597 | 4.3224 | -2.9259 | 5.6719 | 0.0263 | 0.007 | -0.0401 | -0.0458 | -0.0535 | 0.0204 | 0.0077 | -0.0523 | 0.0401 | 0.2422 | -0.0521 | -0.0436 | 0.1941 | -0.11 | 0.1568 | 18.5973 | -17.9013 | -0.4718 | 13 | 2.2154 | -1.1216 | 2.1899 | 0.7581 | -0.7825 | 2.7227 | -0.045 | -0.2073 | 0.1121 | -0.0356 | 0.1134 | 0.1062 | 0.0068 | -0.2724 | -0.0667 | 0.1427 | -0.0492 | -0.1334 | 0.3286 | 0.0559 | 0.571 | 20.9075 | -14.0218 | 0.479 | 14 | 0.0031 | -0.0028 | -0.0241 | 0.11 | -0.0089 | 0.1982 | 0.032 | -0.1085 | 0.0299 | -0.0012 | -0.0068 | 0.0074 | 0.0217 | -0.052 | 0.0313 | 0.1629 | -0.0567 | -0.1994 | 0.2291 | -0.0575 | 0.4883 | 21.871 | -10.3443 | 4.2336 | 15 | 1.9999 | -1.2831 | -1.8739 | 0.7398 | -0.5122 | 3.4896 | 0.0303 | 0.0109 | -0.6397 | 0.033 | 0.039 | 0.264 | 0.0858 | 0.1794 | -0.0753 | 0.1692 | -0.0417 | 0.0476 | 0.3097 | -0.2555 | 0.6296 | 22.4802 | -9.6636 | 9.7323 | 16 | 5.2572 | 4.6507 | -0.3063 | 4.8886 | 0.8138 | 1.5369 | 0.1401 | 0.1628 | -0.5444 | 0.0978 | 0.03 | -0.3484 | 0.2181 | 0.1742 | -0.1586 | 0.3246 | -0.0386 | -0.2534 | 0.4706 | -0.0707 | 0.7696 | 23.969 | -9.8604 | 14.3219 | 17 | 7.2313 | 0.2627 | -6.3227 | 3.2167 | 0.8114 | 8.053 | 0.0782 | -0.0502 | -0.5228 | -0.2636 | 0.3037 | -0.1367 | 1.1484 | 0.5733 | -0.3475 | 0.7599 | 0.1071 | -0.2967 | 0.6795 | -0.1387 | 0.3843 | 26.256 | -12.1398 | 18.5073 | 18 | 4.6322 | -0.3346 | -4.4893 | 2.6333 | 2.2319 | 5.9783 | 0.0602 | -0.72 | -0.3354 | 0.129 | 0.1807 | 0.1302 | 0.3916 | -0.4473 | -0.2291 | 0.6275 | 0.1433 | -0.3984 | 1.0951 | 0.0459 | 0.8068 | 29.0196 | -16.0138 | 21.1866 | 19 | 6.5153 | 4.6419 | -3.8711 | 3.637 | -2.417 | 2.6527 | 0.1485 | -0.7097 | -0.9232 | 0.0826 | -0.0443 | -0.2207 | 0.5504 | 0.5124 | -0.1431 | 0.7358 | 0.1215 | -0.5071 | 0.9809 | 0.1319 | 1.1942 | 32.5617 | -19.3156 | 21.7857 | 20 | 9.1801 | 5.3193 | -5.1447 | 6.2203 | -1.2116 | 3.8809 | -0.2021 | -0.2118 | 0.2296 | -0.3797 | 0.3592 | 1.0234 | 0.6391 | -0.4851 | -0.1611 | 0.7395 | 0.1677 | -0.4716 | 1.2118 | 0.047 | 1.3599 | 37.3625 | -20.8369 | 20.4003 | 21 | 6.7323 | -1.5525 | 1.6102 | 8.0589 | 2.0793 | 5.2745 | 0.0186 | 0.1005 | -0.2355 | 0.0312 | 0.2725 | -0.3147 | 0.1793 | 0.2031 | -0.3723 | 0.5834 | -0.1172 | -0.4409 | 1.1699 | -0.0801 | 0.9168 | 42.5429 | -20.5033 | 19.7163 | 22 | 0.2604 | 0.2811 | 0.3921 | 3.0519 | 3.6278 | 4.7038 | -0.0267 | -0.22 | 0.0578 | 0.2429 | 0.308 | -0.7255 | 0.0687 | 1.0611 | -0.2932 | 0.655 | -0.0912 | -0.4749 | 1.3873 | 0.1404 | 1.4316 | 46.6157 | -18.7134 | 19.9808 | 23 | 3.4353 | 1.204 | -5.0446 | 1.1391 | -1.9192 | 7.4399 | -0.4563 | 0.8661 | -0.8311 | -0.1345 | -0.1492 | -0.0655 | 1.0805 | -0.7017 | 0.5732 | 0.8333 | -0.4639 | -0.1475 | 1.7592 | -0.309 | 1.4868 | 49.4392 | -15.0236 | 21.4914 | 24 | 0.4007 | -0.6811 | 0.3145 | 1.1578 | -0.5346 | 0.2468 | -0.4841 | -0.5006 | 0.8155 | -0.2998 | 0.1386 | 0.7753 | -1.0696 | -0.3237 | 0.3683 | 1.3429 | -0.158 | -0.6343 | 1.2422 | -0.426 | 1.4652 | 43.8396 | -12.524 | 30.3904 | 25 | 4.7157 | -3.2408 | -3.4665 | 9.3009 | 6.8134 | 5.3241 | 0.4031 | -2.2073 | 1.7605 | 2.9076 | 0.1857 | -2.1732 | -0.4923 | 0.7982 | -0.5539 | 1.4336 | 0.163 | -0.4191 | 1.7887 | -0.1121 | 1.5464 | 42.6325 | -10.5755 | 27.4259 | 26 | 5.1798 | 3.7289 | -2.791 | 4.3239 | -1.946 | 1.5063 | 0.1049 | -0.8813 | 1.3042 | 0.5136 | -0.1269 | -0.1995 | -1.1202 | 0.4339 | 0.0338 | 0.9691 | -0.053 | -0.4056 | 1.3344 | -0.071 | 1.4087 | 40.8206 | -8.6321 | 23.5714 | 27 | 5.6922 | 4.5989 | -3.2807 | 2 | -4.1703 | 2 | 1.0816 | -2.0471 | 0.4615 | 1.8393 | -1.2458 | 0.1416 | -0.4155 | 0.4656 | 0.1725 | 1.0054 | -0.1889 | -0.574 | 1.1028 | -0.0656 | 1.3075 | 40.1665 | -9.7929 | 18.1135 | 28 | 9.5883 | -2.7322 | -3.5403 | 1.6962 | -0.1703 | 2.8218 | -0.0972 | -0.4476 | 1.0932 | 0.1542 | -0.0925 | -0.0777 | -0.5118 | 0.7891 | 0.2027 | 0.7922 | -0.0884 | -0.5556 | 0.6674 | -0.0533 | 1.1461 | 39.2059 | -12.4493 | 14.3543 | 29 | 4.0747 | -2.5356 | 2.6025 | 2.4484 | 0.0349 | 5.4478 | -0.0659 | -0.2928 | -0.1682 | 0.0854 | -0.1286 | -0.4962 | 0.0493 | 0.7 | 0.1706 | 0.4156 | 0.0366 | -0.2815 | 0.8508 | 0.1102 | 1.0735 | 36.6974 | -15.9073 | 12.0361 | 30 | 6.7219 | 4.4081 | 2.4361 | 5.0363 | 0.3437 | 2.4558 | 0.2249 | 0.7559 | -1.1173 | 0.0853 | 0.3776 | -1.0222 | 0.5585 | 0.5662 | -0.6488 | 0.3475 | 0.0977 | -0.2588 | 0.4045 | -0.239 | 0.9307 | 32.652 | -18.8205 | 11.1907 | 31 | 7.9958 | -0.4365 | 7.2793 | 6.6215 | -1.9297 | 7.7653 | -0.1864 | 0.2723 | 0.7305 | 0.0617 | 0.1768 | -0.0173 | -0.3517 | -0.495 | -0.0224 | 0.2178 | 0.0118 | -0.1064 | 0.5457 | 0.1378 | 0.7033 | 28.1985 | -20.6703 | 13.1698 | 32 | 9.3102 | 8.2926 | -2.4762 | 7.9543 | -2.6867 | 6.2709 | 0.2072 | -0.5099 | -0.5289 | 0.1025 | -0.2136 | -0.1468 | 0.0891 | 0.5573 | -0.0225 | 0.1474 | 0.0046 | -0.0118 | 0.5629 | -0.1408 | 0.5712 | 24.1391 | -20.2499 | 15.2664 | 33 | 3.294 | 1.9341 | -1.0707 | 6.7749 | -7.3646 | 9.8029 | 0.2687 | -0.7385 | -0.2882 | 0.7461 | -0.0998 | 0.0293 | -0.3012 | -0.2165 | -0.1218 | 0.319 | -0.1077 | -0.1212 | 0.3707 | -0.0051 | 0.2899 | 20.027 | -17.2931 | 14.0615 | 34 | 3.7606 | -2.4318 | -3.456 | 3.0046 | 2.6998 | 3.369 | -0.1257 | -0.4957 | -0.2699 | 0.1617 | 0.3289 | 0.1005 | 0.2679 | 0.103 | -0.1554 | 0.323 | 0.104 | -0.2259 | 0.3251 | 0.0408 | 0.4575 | 16.5514 | -14.4827 | 11.9032 | 35 | 5.4065 | 4.4665 | -0.3808 | 4.2137 | -0.6273 | 2.7527 | 0.0602 | -0.0298 | -0.216 | 0.0021 | 0.118 | -0.1525 | 0.0979 | -0.1372 | -0.0535 | 0.2288 | -0.1143 | -0.0479 | 0.2973 | 0.1443 | 0.3461 | 14.0773 | -11.8865 | 8.537 | 36 | 2.0446 | 0.9202 | 0.132 | 4.8848 | 1.9669 | 1.3316 | 0.1012 | -0.0703 | -0.0036 | 0.3576 | -0.0705 | -0.0842 | 0.2242 | 0.0002 | -0.0078 | 0.3921 | 0.0613 | -0.1633 | 0.3394 | -0.1142 | 0.2429 | 12.6938 | -10.8613 | 3.6116 | 37 | 2.2148 | 1.4455 | -0.9058 | 3.1821 | -2.9438 | 4.1531 | 0.0931 | -0.3999 | 0.0572 | 0.2255 | -0.1473 | 0.1569 | 0.1391 | 0.194 | 0.0147 | 0.3027 | -0.0174 | 0.0427 | 0.1583 | -0.0419 | 0.071 | 11.2752 | -13.1276 | -1.0392 |
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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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