ソフトウェア | 名称 | バージョン | 分類 |
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MAR345dtb | | データ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.8_1069)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.95→29.533 Å / SU ML: 0.23 / σ(F): 0.95 / 位相誤差: 22.73 / 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 | 0.2136 | 3205 | 5.09 % | 5% in each resolution shell |
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Rwork | 0.1735 | - | - | - |
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all | 0.1755 | - | - | - |
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obs | 0.175 | 33803 | 97.34 % | - |
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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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精密化ステップ | サイクル: LAST / 解像度: 1.95→29.533 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3188 | 0 | 2 | 292 | 3482 |
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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_d0.007 | 3330 | X-RAY DIFFRACTION | f_angle_d1.094 | 4517 | X-RAY DIFFRACTION | f_dihedral_angle_d15.055 | 1219 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 477 | X-RAY DIFFRACTION | f_plane_restr0.005 | 590 | | | | | |
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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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1.95-1.9791 | 0.3121 | 131 | 0.3011 | 2477 | X-RAY DIFFRACTION | 91 | 1.9791-2.01 | 0.3397 | 122 | 0.2842 | 2464 | X-RAY DIFFRACTION | 92 | 2.01-2.043 | 0.3339 | 114 | 0.2538 | 2526 | X-RAY DIFFRACTION | 94 | 2.043-2.0782 | 0.279 | 129 | 0.2393 | 2503 | X-RAY DIFFRACTION | 95 | 2.0782-2.116 | 0.2606 | 157 | 0.2236 | 2498 | X-RAY DIFFRACTION | 96 | 2.116-2.1567 | 0.2372 | 160 | 0.2166 | 2620 | X-RAY DIFFRACTION | 96 | 2.1567-2.2007 | 0.2516 | 139 | 0.2067 | 2508 | X-RAY DIFFRACTION | 97 | 2.2007-2.2485 | 0.249 | 147 | 0.2137 | 2661 | X-RAY DIFFRACTION | 97 | 2.2485-2.3008 | 0.2482 | 99 | 0.1983 | 2630 | X-RAY DIFFRACTION | 98 | 2.3008-2.3583 | 0.2596 | 168 | 0.2016 | 2609 | X-RAY DIFFRACTION | 98 | 2.3583-2.4221 | 0.2643 | 164 | 0.2021 | 2617 | X-RAY DIFFRACTION | 99 | 2.4221-2.4933 | 0.2605 | 143 | 0.2053 | 2660 | X-RAY DIFFRACTION | 99 | 2.4933-2.5737 | 0.2555 | 120 | 0.1873 | 2698 | X-RAY DIFFRACTION | 100 | 2.5737-2.6657 | 0.2079 | 133 | 0.1888 | 2675 | X-RAY DIFFRACTION | 100 | 2.6657-2.7723 | 0.2544 | 129 | 0.1986 | 2690 | X-RAY DIFFRACTION | 100 | 2.7723-2.8984 | 0.2301 | 145 | 0.1981 | 2623 | X-RAY DIFFRACTION | 100 | 2.8984-3.051 | 0.2574 | 163 | 0.1928 | 2663 | X-RAY DIFFRACTION | 100 | 3.051-3.242 | 0.2264 | 146 | 0.1926 | 2665 | X-RAY DIFFRACTION | 100 | 3.242-3.4919 | 0.2247 | 158 | 0.1748 | 2627 | X-RAY DIFFRACTION | 100 | 3.4919-3.8427 | 0.195 | 157 | 0.1629 | 2672 | X-RAY DIFFRACTION | 99 | 3.8427-4.3971 | 0.1643 | 147 | 0.1371 | 2608 | X-RAY DIFFRACTION | 99 | 4.3971-5.534 | 0.1587 | 116 | 0.1298 | 2555 | X-RAY DIFFRACTION | 95 | 5.534-29.5368 | 0.1966 | 118 | 0.1607 | 2562 | X-RAY DIFFRACTION | 95 |
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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 | 2.9296 | 1.6779 | 0.6987 | 1.7037 | 0.5467 | 1.8443 | -0.0679 | 0.0477 | -0.4638 | -0.0735 | 0.07 | -0.3268 | 0.1622 | 0.1205 | -0.0114 | 0.1477 | 0.0522 | 0.0272 | 0.4637 | -0.0481 | 0.371 | -9.0477 | 23.6247 | 52.3741 | 2 | 2.6822 | 0.5833 | 0.8207 | 3.7794 | 2.6068 | 5.1544 | -0.0673 | -0.234 | 0.26 | -0.0183 | -0.4126 | 0.6867 | -0.9656 | -0.8982 | 0.363 | 0.383 | 0.1808 | -0.0222 | 0.4858 | -0.1085 | 0.351 | -10.664 | 50.3636 | 76.9515 |
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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 A2 | X-RAY DIFFRACTION | 2 | chain B | |
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