ソフトウェア | 名称 | バージョン | 分類 | NB |
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MOSFLM | | データ削減 | | SCALA | 3.3.20データスケーリング | | PHENIX | 1.8_1069精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | ELVES | | 精密化 | | PHENIX | | 位相決定 | | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.81→74.891 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.19 / σ(F): 1.33 / 位相誤差: 17.63 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2023 | 2418 | 5.15 % |
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Rwork | 0.1613 | - | - |
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obs | 0.1633 | 46968 | 99.69 % |
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all | - | 46969 | - |
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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 mean: 26.6574 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.81→74.891 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3373 | 0 | 5 | 607 | 3985 |
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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_d0.003 | 3562 | X-RAY DIFFRACTION | f_angle_d0.901 | 4868 | X-RAY DIFFRACTION | f_dihedral_angle_d12.56 | 1315 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 562 | X-RAY DIFFRACTION | f_plane_restr0.004 | 625 | | | | | |
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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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1.81-1.847 | 0.2958 | 159 | 0.2593 | 2555 | X-RAY DIFFRACTION | 99 | 1.847-1.8871 | 0.2826 | 136 | 0.2445 | 2577 | X-RAY DIFFRACTION | 100 | 1.8871-1.931 | 0.2747 | 146 | 0.214 | 2563 | X-RAY DIFFRACTION | 99 | 1.931-1.9793 | 0.2451 | 140 | 0.2062 | 2577 | X-RAY DIFFRACTION | 100 | 1.9793-2.0328 | 0.2119 | 146 | 0.1872 | 2583 | X-RAY DIFFRACTION | 99 | 2.0328-2.0927 | 0.2495 | 116 | 0.1793 | 2625 | X-RAY DIFFRACTION | 99 | 2.0927-2.1602 | 0.2052 | 126 | 0.1674 | 2591 | X-RAY DIFFRACTION | 100 | 2.1602-2.2374 | 0.1919 | 159 | 0.1578 | 2578 | X-RAY DIFFRACTION | 100 | 2.2374-2.327 | 0.1886 | 171 | 0.1585 | 2591 | X-RAY DIFFRACTION | 100 | 2.327-2.4329 | 0.2081 | 126 | 0.1581 | 2591 | X-RAY DIFFRACTION | 100 | 2.4329-2.5612 | 0.2137 | 145 | 0.1624 | 2632 | X-RAY DIFFRACTION | 100 | 2.5612-2.7217 | 0.2168 | 139 | 0.1652 | 2616 | X-RAY DIFFRACTION | 100 | 2.7217-2.9318 | 0.1946 | 147 | 0.1602 | 2631 | X-RAY DIFFRACTION | 100 | 2.9318-3.2269 | 0.2035 | 141 | 0.1605 | 2636 | X-RAY DIFFRACTION | 100 | 3.2269-3.6938 | 0.1938 | 145 | 0.1414 | 2672 | X-RAY DIFFRACTION | 100 | 3.6938-4.6537 | 0.1637 | 126 | 0.1249 | 2693 | X-RAY DIFFRACTION | 99 | 4.6537-74.9547 | 0.1682 | 150 | 0.1494 | 2839 | 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 | 0.8308 | 0.4291 | -0.5503 | 0.911 | -1.1012 | 1.4935 | -0.0415 | -0.0527 | -0.032 | -0.0354 | -0.0147 | -0.0331 | 0.0517 | 0.1936 | 0 | 0.1913 | 0.0055 | 0.0072 | 0.2193 | -0.0089 | 0.1979 | 27.3042 | 32.1468 | 47.9518 | 2 | 0.4011 | 0.2435 | 0.7399 | 0.0643 | 0.4438 | 2.0542 | -0.0056 | -0.0143 | 0.0066 | 0.0182 | -0.0041 | -0.0255 | 0.0197 | 0.1069 | 0 | 0.1815 | -0.0002 | 0.0036 | 0.1701 | -0.0059 | 0.1987 | 19.1927 | 34.9952 | 13.4107 | 3 | 0.7982 | 0.6108 | -0.0118 | 1.9868 | 0.7778 | 1.2271 | -0.0189 | -0.0066 | 0.0281 | -0.087 | 0.0691 | -0.0272 | -0.0988 | 0.0318 | -0 | 0.1895 | 0.006 | -0.0117 | 0.1818 | 0.0083 | 0.1855 | 14.2308 | 40.0643 | 51.5657 | 4 | 0.6453 | 0.5558 | -0.4386 | 1.2664 | 0.0143 | 2.4386 | 0.018 | -0.0254 | -0.0364 | -0.0253 | -0.0143 | 0.0557 | 0.1484 | -0.116 | -0 | 0.1623 | -0.0019 | -0.0003 | 0.1915 | -0.0119 | 0.1976 | 0.2348 | 26.2782 | 22.0652 | 5 | 0.1936 | 0.0659 | 0.2026 | 0.155 | -0.0496 | 0.3901 | 0.0651 | 0.4296 | 0.4153 | -0.1734 | 0.0411 | 0.025 | -0.4153 | -0.7668 | 0.0042 | 0.284 | 0.041 | 0.0311 | 0.2898 | 0.0098 | 0.2216 | 4.3084 | 35.3357 | 0.427 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | (chain H and resseq 125:238)2 | X-RAY DIFFRACTION | 2 | (chain H and resseq 1:124)3 | X-RAY DIFFRACTION | 3 | (chain L and resseq 109:214)4 | X-RAY DIFFRACTION | 4 | (chain L and resseq 1:108)5 | X-RAY DIFFRACTION | 5 | (chain P and resseq 1:8) | | | | |
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