ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.1.27データスケーリング | PHENIX | 1.10_2155精密化 | PDB_EXTRACT | 3.27 | データ抽出 | XDS | | データ削減 | PHASER | | 位相決定 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 7N04 解像度: 1.7→45.697 Å / SU ML: 0.23 / 交差検証法: THROUGHOUT / σ(F): 1.91 / 位相誤差: 20.61 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2038 | 2000 | 3.02 % |
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Rwork | 0.1722 | 64223 | - |
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obs | 0.1732 | 66223 | 97.04 % |
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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: 145.24 Å2 / Biso mean: 34.1563 Å2 / Biso min: 14.61 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.7→45.697 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3482 | 0 | 34 | 429 | 3945 |
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Biso mean | - | - | 37.82 | 41.99 | - |
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残基数 | - | - | - | - | 455 |
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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_d0.01 | 3596 | X-RAY DIFFRACTION | f_angle_d1.066 | 4896 | X-RAY DIFFRACTION | f_chiral_restr0.062 | 547 | X-RAY DIFFRACTION | f_plane_restr0.007 | 626 | X-RAY DIFFRACTION | f_dihedral_angle_d12.413 | 2121 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.7-1.7425 | 0.3734 | 111 | 0.3679 | 3556 | 77 | 1.7425-1.7897 | 0.392 | 124 | 0.3374 | 3989 | 86 | 1.7897-1.8423 | 0.3347 | 140 | 0.2896 | 4499 | 96 | 1.8423-1.9018 | 0.2451 | 144 | 0.237 | 4636 | 100 | 1.9018-1.9698 | 0.2457 | 146 | 0.2066 | 4668 | 100 | 1.9698-2.0486 | 0.2292 | 146 | 0.1886 | 4672 | 100 | 2.0486-2.1419 | 0.1983 | 145 | 0.1755 | 4683 | 100 | 2.1419-2.2548 | 0.2174 | 147 | 0.172 | 4703 | 100 | 2.2548-2.3961 | 0.2163 | 146 | 0.1674 | 4717 | 100 | 2.3961-2.581 | 0.2113 | 147 | 0.1727 | 4726 | 100 | 2.581-2.8407 | 0.2082 | 148 | 0.1664 | 4738 | 100 | 2.8407-3.2517 | 0.1612 | 149 | 0.1587 | 4773 | 100 | 3.2517-4.0964 | 0.1815 | 150 | 0.1413 | 4822 | 100 | 4.0964-45.697 | 0.1806 | 157 | 0.1531 | 5041 | 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 | 2.2535 | -2.0137 | -2.3105 | 3.684 | 3.455 | 6.2781 | 0.0132 | 0.0952 | -0.2367 | -0.0844 | -0.2102 | 0.3783 | -0.0674 | -0.3043 | 0.169 | 0.1271 | -0.0274 | 0.0362 | 0.1645 | -0.0361 | 0.243 | -21.429 | 19.751 | -25.818 | 2 | 2.7558 | -0.5714 | -0.8205 | 2.7928 | 1.2262 | 3.2514 | -0.213 | -0.4321 | -0.3731 | 0.4898 | 0.0903 | 0.1651 | 0.3729 | 0.2412 | 0.0726 | 0.2913 | 0.0597 | 0.0988 | 0.2401 | 0.0557 | 0.2611 | -16.496 | 16.777 | -17.596 | 3 | 0.8768 | -0.3253 | 0.1212 | 1.3405 | 0.1156 | 0.592 | -0.0994 | -0.0936 | 0.0588 | 0.0628 | -0.0104 | 0.0428 | -0.063 | -0.0451 | 0.1161 | 0.1571 | 0.0087 | -0.0198 | 0.1944 | -0.0228 | 0.1316 | -17.381 | 39.421 | -20.721 | 4 | 5.2262 | 3.2881 | -1.4614 | 6.3821 | -3.5361 | 5.0787 | -0.0768 | -0.0212 | 0.6525 | 0.0738 | 0.2827 | 0.6168 | -0.367 | -0.5599 | -0.1514 | 0.2085 | 0.043 | -0.0847 | 0.2813 | -0.0394 | 0.2859 | -27.424 | 54.792 | -23.453 | 5 | 1.8789 | -2.0968 | 1.9744 | 7.5435 | -1.7412 | 5.0154 | -0.0461 | -0.0527 | 0.0751 | 0.4289 | 0.0494 | -0.3946 | -0.22 | 0.0695 | 0.018 | 0.0902 | -0.0117 | -0.0278 | 0.2267 | -0.0263 | 0.2379 | 6.486 | 33.033 | -23.185 | 6 | 3.9778 | -1.2884 | 0.2026 | 3.1734 | -0.3263 | 2.6804 | -0.0465 | -0.2479 | -0.3339 | 0.4581 | -0.0617 | -0.6983 | 0.1614 | 0.0952 | 0.0459 | 0.1869 | 0.0306 | 0.0243 | 0.2326 | 0.0364 | 0.2881 | 8.464 | 16.431 | -23.834 | 7 | 7.4163 | -3.9005 | -3.7442 | 4.9041 | 4.5519 | 7.4903 | -0.0387 | 0.1632 | 0.0959 | -0.1612 | -0.1519 | 0.1709 | -0.1994 | -0.2591 | 0.2125 | 0.1406 | -0.0134 | 0.0184 | 0.1215 | -0.0089 | 0.1653 | -4.049 | 27.746 | -29.034 | 8 | 0.8536 | -0.308 | -0.05 | 2.4641 | 0.4398 | 0.9245 | -0.0159 | -0.0026 | 0.0357 | -0.0449 | -0.0847 | -0.2174 | -0.0034 | -0.0194 | 0.0647 | 0.1254 | -0.0105 | -0.0139 | 0.1789 | -0.0008 | 0.1456 | -1.438 | 34.577 | -24.712 | 9 | 4.198 | -2.4538 | -3.4664 | 1.7474 | 2.1506 | 4.3491 | -0.2183 | -0.1344 | 0.1254 | 0.2275 | -0.0079 | -0.0659 | -0.0857 | 0.0182 | 0.1833 | 0.2871 | -0.0079 | -0.0832 | 0.2158 | -0.0708 | 0.2551 | -6.411 | 54.292 | -12.723 | 10 | 1.3504 | -0.417 | -0.7587 | 2.1354 | 1.2998 | 3.6192 | -0.1068 | -0.1667 | 0.2301 | 0.2071 | -0.1036 | -0.1404 | -0.3378 | -0.1173 | -0.018 | 0.2607 | 0.0287 | -0.1279 | 0.2316 | -0.0766 | 0.2258 | -8.818 | 56.761 | -9.324 | 11 | 5.7541 | 2.3922 | -1.9157 | 3.7896 | 3.101 | 6.0749 | 0.1889 | 0.4641 | 0.2855 | -0.1569 | -0.1499 | 0.1678 | -0.2305 | 0.1151 | -0.0433 | 0.2404 | 0.0648 | 0.0273 | 0.1826 | -0.0654 | 0.2735 | -5.445 | 7.975 | -34.026 | 12 | 1.174 | 1.9793 | 1.8901 | 4.665 | 3.6565 | 3.2099 | 0.0414 | 0.938 | -1.402 | -0.4335 | -0.146 | -1.0005 | 1.1847 | 1.0056 | -0.3829 | 0.4527 | 0.1571 | 0.1439 | 0.3913 | -0.0762 | 0.4314 | 2.598 | 6.307 | -36.781 |
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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 H AND RESID 1:33 )H1 - 33 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN H AND RESID 34:87 )H34 - 87 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN H AND RESID 88:188 )H88 - 188 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN H AND RESID 189:213 )H189 - 213 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN L AND RESID 2:18 )L2 - 18 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN L AND RESID 19:32 )L19 - 32 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN L AND RESID 33:48 )L33 - 48 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN L AND RESID 49:128 )L49 - 128 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN L AND RESID 129:150 )L129 - 150 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN L AND RESID 151:212 )L151 - 212 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN E AND RESID 596:603 )E596 - 603 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN E AND RESID 604:610 )E604 - 610 | | | | | | | | | | | | | | | | | | | | | | | | |
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