ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | PDB_EXTRACT | 3.14 | データ抽出 | PHASER | | 位相決定 | PHENIX | (phenix.refine: dev_1760)精密化 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 4N5F 解像度: 1.8→48.199 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 18.69 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1933 | 6533 | 4.97 % |
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Rwork | 0.1598 | 124969 | - |
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obs | 0.1615 | 131502 | 99.67 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 63.24 Å2 / Biso mean: 18.7442 Å2 / Biso min: 5.58 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.8→48.199 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 10965 | 0 | 32 | 1123 | 12120 |
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Biso mean | - | - | 34.43 | 28.22 | - |
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残基数 | - | - | - | - | 1473 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.008 | 11436 | X-RAY DIFFRACTION | f_angle_d1.052 | 15519 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1743 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2061 | X-RAY DIFFRACTION | f_dihedral_angle_d11.913 | 4208 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8-1.8205 | 0.2749 | 221 | 0.2291 | 4186 | 4407 | 100 | 1.8205-1.8419 | 0.2585 | 213 | 0.2123 | 4134 | 4347 | 100 | 1.8419-1.8643 | 0.2451 | 228 | 0.2006 | 4139 | 4367 | 100 | 1.8643-1.8879 | 0.2676 | 226 | 0.1946 | 4177 | 4403 | 100 | 1.8879-1.9128 | 0.2429 | 225 | 0.1914 | 4118 | 4343 | 100 | 1.9128-1.939 | 0.2278 | 212 | 0.1898 | 4144 | 4356 | 100 | 1.939-1.9667 | 0.2272 | 250 | 0.1887 | 4137 | 4387 | 100 | 1.9667-1.996 | 0.2322 | 216 | 0.1833 | 4142 | 4358 | 100 | 1.996-2.0272 | 0.2381 | 227 | 0.1752 | 4188 | 4415 | 100 | 2.0272-2.0605 | 0.1915 | 224 | 0.1708 | 4097 | 4321 | 100 | 2.0605-2.096 | 0.2199 | 235 | 0.1625 | 4129 | 4364 | 100 | 2.096-2.1341 | 0.2233 | 216 | 0.1698 | 4193 | 4409 | 100 | 2.1341-2.1752 | 0.1976 | 220 | 0.1597 | 4138 | 4358 | 100 | 2.1752-2.2196 | 0.1962 | 226 | 0.1549 | 4154 | 4380 | 100 | 2.2196-2.2678 | 0.1967 | 235 | 0.1527 | 4149 | 4384 | 100 | 2.2678-2.3206 | 0.198 | 192 | 0.1575 | 4145 | 4337 | 100 | 2.3206-2.3786 | 0.1839 | 221 | 0.1544 | 4169 | 4390 | 100 | 2.3786-2.4429 | 0.2059 | 182 | 0.1618 | 4188 | 4370 | 100 | 2.4429-2.5148 | 0.2075 | 205 | 0.1648 | 4160 | 4365 | 100 | 2.5148-2.596 | 0.1888 | 233 | 0.1609 | 4164 | 4397 | 100 | 2.596-2.6887 | 0.19 | 204 | 0.1574 | 4180 | 4384 | 100 | 2.6887-2.7964 | 0.1856 | 192 | 0.1577 | 4161 | 4353 | 100 | 2.7964-2.9236 | 0.1906 | 214 | 0.1623 | 4169 | 4383 | 100 | 2.9236-3.0778 | 0.1968 | 223 | 0.1635 | 4172 | 4395 | 100 | 3.0778-3.2705 | 0.1789 | 216 | 0.1635 | 4180 | 4396 | 100 | 3.2705-3.523 | 0.1802 | 227 | 0.159 | 4167 | 4394 | 100 | 3.523-3.8774 | 0.1727 | 232 | 0.141 | 4164 | 4396 | 100 | 3.8774-4.4381 | 0.1574 | 192 | 0.1295 | 4229 | 4421 | 100 | 4.4381-5.5902 | 0.156 | 207 | 0.1382 | 4223 | 4430 | 100 | 5.5902-48.2164 | 0.1642 | 219 | 0.1524 | 4273 | 4492 | 99 |
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精密化 TLS | 手法: 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 | 1.601 | 0.6634 | -1.5368 | 1.1354 | -0.8852 | 1.7808 | 0.1215 | -0.2518 | 0.1169 | 0.0908 | -0.0795 | 0.1075 | -0.1133 | -0.0863 | -0.0395 | 0.1731 | 0.0166 | -0.0133 | 0.1766 | -0.006 | 0.1428 | 22.6507 | -13.1048 | 50.0817 | 2 | 0.6904 | -0.0945 | -0.1575 | 0.5217 | -0.0897 | 0.9858 | -0.0001 | -0.1097 | -0.0477 | 0.0287 | -0.0286 | 0.0201 | 0.1414 | 0.1068 | 0.0419 | 0.1201 | 0.0337 | -0.0031 | 0.1228 | 0.0257 | 0.1023 | 34.5752 | -18.5458 | 39.911 | 3 | 0.6152 | -0.0068 | 0.2475 | 0.7538 | 0.165 | 0.14 | -0.0024 | 0.0012 | -0.2026 | -0.0211 | 0.0225 | -0.0901 | 0.374 | 0.2978 | -0.0063 | 0.2682 | 0.0978 | 0.0159 | 0.1761 | 0.0054 | 0.1478 | 41.9415 | -30.87 | 28.883 | 4 | 0.9964 | -0.3149 | -0.1729 | 1.5479 | 0.1136 | 0.6885 | -0.0619 | 0.1213 | -0.1405 | -0.0447 | 0.0647 | -0.0814 | 0.2995 | 0.1874 | -0.0067 | 0.2065 | 0.0709 | -0.0049 | 0.1684 | -0.0227 | 0.104 | 40.4293 | -28.5695 | 24.1515 | 5 | 0.3843 | 0.4171 | 0.0904 | 5.4606 | 0.6626 | 0.7222 | 0.0659 | -0.0552 | -0.0016 | 0.3013 | -0.0418 | -0.1445 | 0.0097 | 0.0335 | 0.0074 | 0.0891 | -0.0007 | 0.006 | 0.13 | 0.0126 | 0.0962 | 24.4497 | -4.4926 | 36.5088 | 6 | 1.3167 | 0.4026 | 0.1357 | 2.4134 | 0.3688 | 0.7433 | 0.0182 | -0.0769 | 0.0905 | 0.0302 | -0.0865 | 0.1905 | -0.1055 | -0.005 | 0.0611 | 0.1125 | -0.0005 | 0.001 | 0.1193 | 0.0026 | 0.0891 | 15.9238 | -1.1775 | 37.6028 | 7 | 0.5668 | 0.2333 | 0.1065 | 1.8972 | -0.1486 | 0.7407 | -0.0066 | -0.03 | -0.0206 | 0.0346 | 0.0047 | 0.0133 | -0.0186 | 0.0398 | 0.0084 | 0.0853 | 0.0106 | 0.0042 | 0.1153 | 0.0049 | 0.0832 | 25.2823 | -4.6273 | 29.5157 | 8 | 6.2238 | 1.1346 | 1.9156 | 3.6473 | 0.586 | 3.4982 | 0.0373 | 0.1282 | -0.3947 | -0.0437 | -0.0267 | 0.0557 | 0.1637 | -0.0487 | -0.0361 | 0.1351 | 0.0121 | 0.0028 | 0.0904 | -0.0026 | 0.1266 | 19.916 | -18.7262 | 21.0986 | 9 | 3.7888 | -1.8915 | 2.1549 | 1.8655 | -1.2536 | 2.3113 | 0.1367 | 0.2776 | 0.0075 | -0.317 | -0.1173 | 0.0455 | 0.1871 | -0.0052 | -0.0047 | 0.2398 | -0.0021 | 0.0032 | 0.1667 | 0.0034 | 0.1515 | 29.9832 | 13.6011 | -4.4375 | 10 | 1.0831 | 0.5894 | -0.1188 | 1.0857 | -0.1555 | 1.6333 | 0.0486 | -0.0035 | -0.117 | -0.0355 | -0.0958 | -0.1566 | 0.1238 | 0.2876 | 0.0552 | 0.1049 | 0.0151 | 0.0087 | 0.159 | 0.0191 | 0.1745 | 45.6971 | 10.7449 | 10.6995 | 11 | 0.2312 | 0.1421 | 0.0679 | 1.1419 | 0.1209 | 0.9946 | 0.0089 | 0.0424 | 0.0603 | -0.0871 | 0.0041 | -0.0214 | -0.1552 | 0.0551 | 0.0054 | 0.108 | -0.0156 | 0.0103 | 0.1112 | 0.0187 | 0.1182 | 34.8553 | 23.1933 | 6.8164 | 12 | 0.951 | -0.1153 | 0.1513 | 1.4434 | 0.7013 | 1.5263 | -0.0201 | -0.0069 | 0.1154 | 0.0938 | 0.0364 | -0.1035 | -0.2248 | 0.1456 | -0.0247 | 0.1437 | -0.0371 | -0.0138 | 0.1282 | 0.001 | 0.1382 | 41.792 | 31.1923 | 20.6818 | 13 | 1.3203 | -0.5449 | 0.4122 | 2.1566 | 0.2111 | 1.107 | -0.0273 | -0.0723 | 0.1839 | 0.1796 | 0.0157 | -0.1376 | -0.0987 | -0.0197 | 0.0006 | 0.1716 | -0.0388 | 0.0027 | 0.1382 | -0.0114 | 0.1137 | 40.0741 | 31.5719 | 26.4884 | 14 | 0.5353 | 0.5051 | 0.2725 | 1.8203 | 0.2991 | 0.4477 | 0.0072 | -0.0112 | 0.0844 | 0.0501 | -0.0172 | -0.0786 | -0.0939 | 0.0342 | 0.0124 | 0.1513 | -0.0146 | 0.0111 | 0.1422 | 0.001 | 0.1342 | 38.2569 | 28.381 | 23.4594 | 15 | 0.6599 | -0.1794 | 0.0418 | 5.1865 | 1.8883 | 1.1187 | 0.0185 | 0.0455 | 0.0126 | -0.0737 | 0.0035 | -0.1205 | 0.0173 | 0.0661 | 0.0106 | 0.0902 | 0.004 | 0.0028 | 0.1236 | 0.0229 | 0.0727 | 28.5576 | 4.5035 | 9.0292 | 16 | 0.7959 | 0.1292 | 0.0523 | 1.9634 | -0.0563 | 0.347 | -0.0266 | 0.0636 | -0.0983 | 0.038 | 0.0343 | 0.1647 | 0.018 | -0.0016 | -0.0062 | 0.0951 | -0.0003 | -0.0028 | 0.1129 | -0.0045 | 0.0975 | 20.6153 | 0.65 | 5.2989 | 17 | 0.4179 | -0.2534 | -0.1217 | 1.5956 | -0.3804 | 0.5043 | -0.0048 | 0.0364 | 0.0361 | 0.0599 | -0.0043 | 0.0781 | -0.0439 | -0.0078 | -0.0065 | 0.0911 | -0.0094 | -0.0148 | 0.1197 | 0.0007 | 0.1032 | 20.9876 | 10.6583 | 14.0826 | 18 | 0.4687 | 0.288 | 0.3639 | 1.9155 | -0.3327 | 1.138 | 0.0324 | 0.0918 | -0.0402 | -0.1825 | -0.0517 | -0.1468 | 0.0617 | 0.1912 | 0.0463 | 0.1046 | 0.0117 | 0.0165 | 0.1307 | 0.0159 | 0.1097 | 33.7521 | -1.9741 | 17.1368 | 19 | 7.3702 | -2.5431 | -0.061 | 3.13 | 0.233 | 1.3307 | -0.12 | -0.1929 | 0.4197 | 0.1962 | 0.115 | 0.0239 | -0.0634 | -0.1779 | 0.0292 | 0.1286 | -0.0011 | 0.0062 | 0.1111 | -0.0073 | 0.1131 | 18.4337 | 18.8033 | 22.1043 | 20 | 4.3229 | -0.1233 | 3.1401 | 1.3697 | 0.1438 | 4.1946 | 0.3148 | 0.0853 | -0.2456 | 0.181 | -0.0787 | -0.0097 | 0.523 | 0.1737 | -0.2741 | 0.2639 | 0.0014 | 0.0037 | 0.1392 | -0.0008 | 0.1892 | 72.0781 | -23.8185 | 37.3879 | 21 | 1.264 | -0.0578 | -0.4225 | 2.189 | -0.5471 | 1.9244 | 0.0401 | 0.0618 | -0.0661 | -0.1111 | 0.0034 | 0.1703 | 0.2024 | -0.2029 | -0.0384 | 0.1311 | -0.0099 | -0.0197 | 0.1356 | -0.013 | 0.1559 | 56.0899 | -13.1546 | 28.5211 | 22 | 1.2821 | -0.0459 | -0.2955 | 1.3753 | -0.0008 | 1.4647 | -0.0617 | -0.1585 | -0.0729 | 0.2435 | 0.0135 | 0.1209 | 0.0767 | 0.0042 | 0.0551 | 0.1524 | 0.0094 | 0.0229 | 0.1332 | 0.0173 | 0.1423 | 66.3219 | -16.2693 | 43.2519 | 23 | 1.0221 | -0.5685 | -0.6289 | 1.4988 | 0.8301 | 3.7678 | -0.0379 | -0.1249 | -0.1 | 0.2089 | -0.0242 | 0.0695 | 0.1581 | 0.0589 | 0.06 | 0.0959 | -0.0184 | 0.0099 | 0.1221 | 0.0129 | 0.1237 | 63.1222 | -6.9665 | 44.0391 | 24 | 1.2402 | -0.3134 | -0.1384 | 1.8943 | 0.3405 | 1.6299 | -0.0466 | -0.1794 | 0.0608 | 0.2065 | -0.0583 | 0.1963 | -0.1364 | -0.1195 | 0.1029 | 0.1395 | 0.0132 | 0.0104 | 0.1695 | -0.0349 | 0.146 | 54.9504 | 1.7579 | 46.8327 | 25 | 0.831 | -0.6422 | 0.1345 | 0.908 | 0.1115 | 2.1642 | -0.0139 | -0.0387 | 0.0685 | -0.0129 | -0.0431 | 0.1142 | -0.306 | -0.0452 | 0.0792 | 0.1682 | -0.0062 | 0.0149 | 0.1557 | -0.0292 | 0.1652 | 55.1909 | 7.3206 | 46.4197 | 26 | 0.8786 | -0.2568 | -0.3199 | 0.6564 | 0.7253 | 2.4745 | -0.0543 | -0.0937 | 0.0621 | 0.1095 | -0.111 | 0.1075 | -0.1623 | -0.164 | 0.1643 | 0.1459 | -0.0089 | 0.0132 | 0.1274 | -0.0139 | 0.1482 | 58.16 | 3.8916 | 43.7982 | 27 | 0.9405 | -0.3963 | -0.8145 | 1.4103 | 1.65 | 2.5985 | -0 | 0.0593 | -0.1363 | -0.0868 | -0.0762 | 0.106 | 0.0086 | -0.1491 | 0.0634 | 0.0995 | 0.0001 | -0.0132 | 0.0814 | 0.027 | 0.1323 | 75.5261 | -15.5362 | 22.6168 | 28 | 0.6748 | -0.166 | -1.1681 | 0.2585 | 0.8373 | 5.0543 | -0.0226 | -0.0466 | 0.0171 | 0.0252 | 0.0509 | -0.0534 | 0.0747 | 0.0502 | -0.0536 | 0.1126 | -0.0042 | -0.018 | 0.1166 | 0.0107 | 0.1579 | 83.7018 | -14.0814 | 26.7631 | 29 | 0.3642 | 0.1094 | 0.0441 | 0.3074 | 0.191 | 1.9808 | 0.0104 | -0.0062 | -0.0307 | -0.001 | 0.0227 | -0.0053 | 0.0754 | -0.0467 | -0.0473 | 0.1162 | 0.0021 | -0.0008 | 0.0882 | 0.0139 | 0.1266 | 74.5177 | -6.522 | 24.9195 | 30 | 6.5391 | 1.2083 | 1.3031 | 2.117 | 0.3789 | 2.2917 | -0.01 | -0.422 | 0.2905 | 0.0818 | -0.0748 | 0.0037 | -0.0667 | 0.0577 | 0.1147 | 0.1203 | 0.0145 | 0.0059 | 0.1153 | -0.0199 | 0.1168 | 79.4824 | 4.6627 | 38.0124 | 31 | 0.8719 | 0.2264 | -0.1743 | 1.3075 | -0.4337 | 1.2877 | -0.0319 | 0.0379 | 0.1434 | -0.0232 | 0.0577 | 0.0555 | -0.0667 | -0.0136 | -0.0334 | 0.1335 | 0.0195 | -0.0104 | 0.1169 | 0.025 | 0.1441 | 69.4706 | 15.3302 | -1.8778 | 32 | 0.6527 | 0.0214 | -0.289 | 1.5567 | 0.4928 | 1.3519 | -0.0515 | 0.1345 | -0.0171 | -0.1748 | 0.0268 | 0.072 | 0.0753 | -0.1093 | 0.0177 | 0.1429 | -0.0153 | -0.0328 | 0.1736 | 0.018 | 0.1546 | 66.4139 | -2.3744 | -12.5805 | 33 | 0.3996 | 0.2596 | 0.0514 | 0.6889 | 0.5312 | 1.7304 | -0.039 | 0.0397 | -0.0331 | -0.0609 | 0.0171 | 0.0427 | 0.029 | -0.12 | 0.0179 | 0.1023 | 0.0065 | -0.0133 | 0.1013 | 0.0264 | 0.1536 | 69.0834 | -2.6185 | -4.7687 | 34 | 1.2229 | 0.3614 | -0.2719 | 0.835 | 0.8043 | 6.5436 | -0.0221 | -0.1344 | 0.047 | 0.1604 | -0.0413 | 0.05 | 0.0609 | 0.1324 | 0.0574 | 0.1413 | 0.0115 | 0.0014 | 0.09 | 0.019 | 0.16 | 83.8751 | 13.5473 | 13.1103 | 35 | 0.6206 | -0.038 | -0.5203 | 0.3606 | 0.0884 | 2.2384 | 0.0548 | 0.0267 | 0.0693 | -0.0009 | 0.0083 | 0.0036 | -0.115 | -0.0736 | -0.0891 | 0.0999 | 0.0033 | -0.012 | 0.0722 | 0.0103 | 0.1323 | 76.0217 | 4.9778 | 12.5859 | 36 | 5.9661 | -1.1894 | -1.0341 | 2.3359 | 0.3777 | 2.7754 | -0.0135 | 0.4204 | -0.1671 | -0.0829 | -0.0162 | -0.0779 | 0.1012 | 0.1173 | 0.0252 | 0.1124 | -0.0008 | 0.0039 | 0.1011 | -0.0134 | 0.0726 | 85.2335 | -5.5964 | 1.7172 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid -3 through 21 ) | A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 22 through 101 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 102 through 162 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 163 through 236 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 237 through 266 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 267 through 305 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 306 through 358 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 359 through 375 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid -2 through 21 ) | B0 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 22 through 46 )B0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 47 through 101 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 102 through 162 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 163 through 196 )B0 | 14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 197 through 236 )B0 | 15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid | | | | | | | | | | | | | | | | | | | | | | | | | | |
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