ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | PHASER | | 位相決定 | PHENIX | | 精密化 | PDB_EXTRACT | 3.22 | データ抽出 |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1U7G 解像度: 2.45→56.219 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.04
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2125 | 1079 | 5.01 % | Random Selection |
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Rwork | 0.1699 | - | - | - |
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obs | 0.1719 | 21556 | 98.63 % | - |
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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 |
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原子変位パラメータ | Biso max: 239.47 Å2 / Biso mean: 61.6964 Å2 / Biso min: 27.83 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.45→56.219 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2648 | 0 | 107 | 77 | 2832 |
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Biso mean | - | - | 95.4 | 64.57 | - |
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残基数 | - | - | - | - | 369 |
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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_d0.002 | 2817 | X-RAY DIFFRACTION | f_angle_d0.618 | 3834 | X-RAY DIFFRACTION | f_chiral_restr0.02 | 452 | X-RAY DIFFRACTION | f_plane_restr0.003 | 460 | X-RAY DIFFRACTION | f_dihedral_angle_d18.294 | 923 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.4501-2.5616 | 0.2655 | 134 | 0.2206 | 2532 | 2666 | 99 | 2.5616-2.6966 | 0.2246 | 134 | 0.1933 | 2552 | 2686 | 100 | 2.6966-2.8656 | 0.2085 | 134 | 0.1761 | 2538 | 2672 | 99 | 2.8656-3.0868 | 0.2212 | 135 | 0.1635 | 2580 | 2715 | 99 | 3.0868-3.3974 | 0.2137 | 135 | 0.1676 | 2556 | 2691 | 99 | 3.3974-3.8889 | 0.2095 | 134 | 0.1656 | 2546 | 2680 | 98 | 3.8889-4.8992 | 0.1803 | 135 | 0.1552 | 2565 | 2700 | 98 | 4.8992-56.2336 | 0.2334 | 138 | 0.1752 | 2608 | 2746 | 96 |
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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 | 0.573 | 0.1562 | -0.2463 | 0.3852 | -0.1183 | 0.1078 | -0.0922 | -0.0269 | 0.0868 | -0.0127 | -0.1073 | -0.1447 | -0.1815 | -0.0413 | -0 | 0.4066 | -0.0113 | 0.0109 | 0.3542 | 0.0322 | 0.3668 | 7.8625 | 9.9813 | 51.584 | 2 | 0.5037 | -0.3333 | -0.344 | 1.0299 | -0.2247 | 0.4564 | -0.0406 | -0.0484 | 0.1056 | -0.0004 | -0.0545 | -0.1176 | -0.1243 | 0.0133 | -0 | 0.4441 | -0.0391 | 0.0165 | 0.3807 | 0.0169 | 0.4706 | 10.1293 | 21.2967 | 56.0514 | 3 | 0.2658 | 0.1789 | 0.0412 | 0.5146 | 0.3098 | 0.1842 | -0.041 | -0.0054 | 0.1523 | -0.0441 | -0.0002 | 0.0992 | -0.1397 | 0.002 | 0 | 0.4104 | 0.0272 | -0.0289 | 0.394 | 0.0409 | 0.4231 | -10.9606 | 15.4241 | 50.3704 | 4 | 0.5581 | 0.3476 | 0.1221 | 0.3543 | -0.0361 | 0.1199 | 0.1213 | -0.1109 | 0.1873 | 0.0314 | 0.0521 | -0.0446 | -0.3567 | 0.3331 | 0.0003 | 0.6345 | 0.014 | -0.0001 | 0.481 | 0.1006 | 0.6092 | -9.3172 | 26.5764 | 56.5198 | 5 | 0.4571 | -0.2637 | -0.0784 | 0.1951 | -0.0674 | 0.3156 | 0.2998 | -0.2332 | 0.4512 | -0.1639 | -0.0291 | -0.0343 | -0.7774 | 0.3779 | 0.0069 | 0.6859 | -0.0368 | 0.0839 | 0.4263 | 0.0832 | 0.4744 | 6.5526 | 32.2812 | 50.4061 |
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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 1 through 61 )A1 - 61 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 62 through 197 )A62 - 197 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 198 through 301 )A198 - 301 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 302 through 347 )A302 - 347 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 348 through 385 )A348 - 385 | | | | | | | | | | |
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