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 | XSCALE | | データスケーリング | PHENIX | dev_2276精密化 | PHASER | | 位相決定 | PDB_EXTRACT | | データ抽出 | Coot | | モデル構築 | |
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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 4nt8 解像度: 1.6→50 Å / SU ML: 0.14 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 18.86 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1784 | 2107 | 3.15 % | Random selection |
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Rwork | 0.1536 | 64697 | - | - |
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obs | 0.1544 | 66804 | 99.84 % | - |
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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: 69.84 Å2 / Biso mean: 17.5828 Å2 / Biso min: 3.72 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.6→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2738 | 0 | 58 | 586 | 3382 |
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Biso mean | - | - | 31.78 | 29.42 | - |
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残基数 | - | - | - | - | 348 |
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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_d0.012 | 3019 | X-RAY DIFFRACTION | f_angle_d1.18 | 4116 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 428 | X-RAY DIFFRACTION | f_plane_restr0.008 | 538 | X-RAY DIFFRACTION | f_dihedral_angle_d14.438 | 1846 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.6-1.6372 | 0.2464 | 144 | 0.2104 | 4190 | X-RAY DIFFRACTION | 99 | 1.6372-1.6782 | 0.247 | 157 | 0.194 | 4251 | X-RAY DIFFRACTION | 99 | 1.6782-1.7235 | 0.2307 | 122 | 0.1789 | 4295 | X-RAY DIFFRACTION | 100 | 1.7235-1.7743 | 0.1816 | 117 | 0.1675 | 4291 | X-RAY DIFFRACTION | 100 | 1.7743-1.8315 | 0.2 | 147 | 0.1586 | 4272 | X-RAY DIFFRACTION | 100 | 1.8315-1.897 | 0.1988 | 143 | 0.1571 | 4265 | X-RAY DIFFRACTION | 100 | 1.897-1.9729 | 0.1815 | 128 | 0.1615 | 4325 | X-RAY DIFFRACTION | 100 | 1.9729-2.0627 | 0.1776 | 128 | 0.1437 | 4295 | X-RAY DIFFRACTION | 100 | 2.0627-2.1715 | 0.1604 | 126 | 0.141 | 4335 | X-RAY DIFFRACTION | 100 | 2.1715-2.3075 | 0.1928 | 136 | 0.1439 | 4294 | X-RAY DIFFRACTION | 100 | 2.3075-2.4857 | 0.187 | 161 | 0.1458 | 4297 | X-RAY DIFFRACTION | 100 | 2.4857-2.7358 | 0.1636 | 157 | 0.161 | 4315 | X-RAY DIFFRACTION | 100 | 2.7358-3.1316 | 0.1889 | 145 | 0.1616 | 4356 | X-RAY DIFFRACTION | 100 | 3.1316-3.9452 | 0.1515 | 131 | 0.1419 | 4395 | X-RAY DIFFRACTION | 100 | 3.9452-50 | 0.1569 | 165 | 0.1424 | 4521 | X-RAY DIFFRACTION | 100 |
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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 | 4.7975 | -3.4166 | -1.0347 | 3.2306 | 0.9069 | 1.5541 | 0.0282 | 0.0925 | 0.2131 | -0.1993 | -0.0867 | -0.607 | 0.1399 | 0.0666 | -0.0008 | 0.1375 | 0.0311 | 0.067 | 0.1121 | 0.0172 | 0.2143 | 28.5977 | 46.3039 | 7.3144 | 2 | 1.6288 | -1.0923 | -0.1183 | 2.2493 | 0.8565 | 0.5027 | 0.1713 | 0.2474 | -0.1189 | -0.1963 | -0.0763 | 0.1252 | 0.0866 | 0.101 | -0.0487 | 0.1786 | 0.0565 | -0.0278 | 0.1292 | -0.0223 | 0.0755 | 15.9536 | 39.0029 | 2.3973 | 3 | 2.4898 | 0.564 | 1.0917 | 4.2584 | 2.7725 | 4.1833 | 0.1989 | 0.0884 | -0.0531 | -0.1837 | -0.0518 | -0.2117 | 0.021 | 0.0447 | -0.168 | 0.0992 | 0.0459 | -0.0037 | 0.0852 | -0.0029 | 0.1026 | 27.7272 | 34.7565 | 9.1369 | 4 | 1.3903 | -0.0866 | 0.1567 | 1.1511 | 0.3068 | 1.2682 | 0.0737 | -0.0192 | 0.0117 | 0.07 | 0.0074 | -0.0448 | 0.0907 | 0.1633 | -0.0865 | 0.1123 | 0.029 | -0.0006 | 0.1017 | -0.0086 | 0.0927 | 21.5324 | 38.8743 | 14.2845 | 5 | 0.7012 | 0.1896 | -0.4045 | 3.1293 | 0.7074 | 2.6207 | 0.0788 | 0.116 | -0.0023 | -0.0848 | -0.0615 | -0.0943 | 0.0673 | 0.1822 | -0.0193 | 0.1052 | 0.0435 | -0.021 | 0.122 | -0.0031 | 0.0956 | 21.9834 | 39.7287 | 27.6175 | 6 | 3.3281 | -2.0759 | -2.7854 | 2.2067 | 1.0717 | 2.9155 | 0.0235 | 0.2563 | -0.2063 | 0.0205 | -0.0951 | 0.1258 | 0.0318 | -0.1393 | 0.058 | 0.0957 | -0.0029 | -0.0172 | 0.0647 | -0.0155 | 0.0879 | 10.4548 | 32.7061 | 13.567 | 7 | 4.4239 | 2.2858 | 0.0446 | 2.2419 | 0.0654 | 0.759 | 0.1443 | -0.209 | -0.0036 | 0.0023 | -0.1277 | 0.0048 | 0.0352 | -0.0211 | -0.0132 | 0.0708 | 0.0106 | -0.0037 | 0.0651 | 0.0006 | 0.0688 | 11.9189 | 47.0986 | 23.5875 | 8 | 4.0023 | -2.2452 | -2.9969 | 2.5582 | 2.8669 | 3.7025 | -0.0112 | 0.153 | -0.5224 | 0.1174 | -0.2456 | 0.1856 | 0.0587 | -0.108 | 0.2647 | 0.1193 | 0.0252 | -0.0235 | 0.0725 | -0.0156 | 0.1468 | 11.4244 | 28.4871 | 14.6475 | 9 | 1.2511 | 0.2878 | -0.316 | 1.8486 | 1.1281 | 2.1166 | 0.0788 | 0.0124 | -0.1929 | 0.0862 | -0.0622 | -0.1253 | 0.1343 | 0.0792 | -0.0028 | 0.0616 | 0.0164 | -0.013 | 0.0655 | -0.0071 | 0.1161 | 11.8925 | 36.2896 | 18.2266 | 10 | 1.4933 | -0.3715 | -0.4449 | 1.032 | 0.7857 | 3.9496 | 0.0545 | 0.0559 | 0.1714 | -0.1402 | -0.195 | 0.2268 | -0.279 | -0.2581 | 0.0616 | 0.1277 | 0.008 | 0.0159 | 0.0784 | -0.004 | 0.1388 | 10.2435 | 53.5043 | 19.9355 | 11 | 4.2555 | -2.2836 | -1.3449 | 6.8346 | -0.0488 | 2.8835 | 0.2502 | -0.2656 | -0.2181 | 0.2226 | -0.0358 | -0.5023 | 0.2795 | 0.3732 | 0.0079 | 0.1092 | -0.0148 | -0.0253 | 0.1164 | 0.009 | 0.1567 | 23.0096 | 55.7107 | 28.1705 | 12 | 5.4553 | 4.2897 | 0.4757 | 4.1313 | 0.2181 | 0.7534 | 0.1134 | -0.0377 | -0.1886 | 0.1945 | -0.3112 | -0.8679 | -0.1517 | 0.0643 | -0.1381 | 0.1144 | -0.0437 | -0.0639 | 0.0995 | 0.0592 | 0.2713 | 28.5457 | 70.7721 | 28.919 | 13 | 1.11 | 0.6222 | -0.3435 | 1.784 | -0.1567 | 0.7113 | 0.0971 | -0.022 | 0.021 | 0.1279 | -0.1182 | -0.0986 | -0.1096 | 0.0905 | 0.0258 | 0.0921 | -0.0281 | -0.0195 | 0.0959 | 0.017 | 0.0721 | 22.4079 | 81.1348 | 30.3277 | 14 | 1.7999 | -0.3721 | 0.3247 | 2.4418 | 0.1131 | 0.8072 | -0.0082 | 0.3411 | 0.0343 | -0.2548 | -0.0175 | -0.0793 | -0.0766 | 0.1566 | -0.0477 | 0.1023 | -0.034 | 0.0045 | 0.1326 | 0.0111 | 0.0868 | 21.3668 | 78.0383 | 22.0596 | 15 | 4.5715 | -0.8907 | -2.2694 | 8.91 | -1.3663 | 1.7104 | -0.0807 | 0.5088 | -0.1693 | -0.9671 | -0.3271 | -0.7203 | 0.4634 | -0.1267 | -0.1324 | 0.3857 | -0.0799 | 0.0251 | 0.4279 | 0.0313 | 0.2162 | 22.2452 | 76.9643 | 8.419 | 16 | 3.0838 | 1.7042 | 2.7574 | 2.3344 | 1.3713 | 2.4543 | -0.0491 | -0.1312 | 0.2701 | -0.0632 | -0.1142 | 0.1611 | -0.0552 | -0.105 | 0.1543 | 0.078 | -0.0012 | -0.0116 | 0.0732 | 0.0028 | 0.0815 | 10.4518 | 84.2634 | 22.2926 | 17 | 3.9348 | -1.847 | 0.568 | 1.7309 | -0.4399 | 0.992 | 0.1676 | 0.2779 | -0.0097 | -0.0918 | -0.1478 | 0.0055 | 0.0538 | 0.0992 | 0.0616 | 0.0899 | 0.0132 | -0.0032 | 0.088 | -0.008 | 0.0808 | 12.0258 | 69.7792 | 12.5387 | 18 | 4.1016 | 2.4892 | 2.9416 | 2.1526 | 2.3435 | 2.8025 | -0.0631 | -0.0297 | 0.3668 | -0.1399 | -0.1471 | 0.261 | -0.1338 | -0.036 | 0.3342 | 0.114 | -0.0097 | -0.0199 | 0.075 | 0.0113 | 0.1239 | 11.1692 | 88.2606 | 20.5229 | 19 | 1.1481 | 0.0064 | 0.3556 | 2.2249 | 1.0856 | 1.5907 | 0.0198 | 0.0482 | 0.0919 | -0.0826 | -0.0845 | 0.0314 | -0.0636 | 0.0465 | -0.0232 | 0.0501 | 0.0027 | -0.0116 | 0.0747 | 0.0023 | 0.0901 | 11.3865 | 76.0179 | 17.9899 | 20 | 6.8678 | 2.1739 | -1.516 | 3.3373 | -0.9491 | 1.4634 | 0.0226 | 0.3165 | -0.0935 | -0.2836 | -0.0564 | -0.3646 | -0.0328 | 0.2014 | 0.153 | 0.1687 | 0.0303 | 0.0132 | 0.1201 | 0.0093 | 0.1173 | 19.5343 | 60.6726 | 8.4428 |
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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 -2 through 10 ) | A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 11 through 25 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 26 through 41 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 42 through 66 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 67 through 76 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 77 through 87 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 88 through 112 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 113 through 125 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 126 through 147 )A0 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 148 through 160 )A0 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 161 through 171 )A0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid -2 through 10 ) | B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 11 through 41 )B0 | 14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 42 through 66 )B0 | 15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid | | | | | | | | | | | | | | | | | | | | | | | | | | |
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