ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.8.4_1496精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | MLPHARE | | 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: 1.76→37.539 Å / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 19.95 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2218 | 2171 | 5.04 % |
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Rwork | 0.1812 | - | - |
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obs | 0.1832 | 43049 | 97.57 % |
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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: 1.76→37.539 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2969 | 0 | 7 | 213 | 3189 |
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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_d0.008 | 3063 | X-RAY DIFFRACTION | f_angle_d1.04 | 4177 | X-RAY DIFFRACTION | f_dihedral_angle_d13.694 | 1106 | X-RAY DIFFRACTION | f_chiral_restr0.043 | 489 | X-RAY DIFFRACTION | f_plane_restr0.006 | 537 | | | | | |
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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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1.7595-1.7978 | 0.2897 | 134 | 0.2459 | 2425 | X-RAY DIFFRACTION | 94 | 1.7978-1.8396 | 0.2888 | 147 | 0.2192 | 2466 | X-RAY DIFFRACTION | 99 | 1.8396-1.8856 | 0.2457 | 133 | 0.2105 | 2571 | X-RAY DIFFRACTION | 99 | 1.8856-1.9366 | 0.2462 | 138 | 0.2025 | 2565 | X-RAY DIFFRACTION | 99 | 1.9366-1.9936 | 0.2179 | 145 | 0.1922 | 2534 | X-RAY DIFFRACTION | 99 | 1.9936-2.0579 | 0.2335 | 133 | 0.191 | 2545 | X-RAY DIFFRACTION | 99 | 2.0579-2.1314 | 0.1932 | 138 | 0.1835 | 2529 | X-RAY DIFFRACTION | 98 | 2.1314-2.2168 | 0.2217 | 141 | 0.1745 | 2546 | X-RAY DIFFRACTION | 98 | 2.2168-2.3176 | 0.2251 | 134 | 0.1785 | 2588 | X-RAY DIFFRACTION | 99 | 2.3176-2.4398 | 0.2291 | 125 | 0.1782 | 2565 | X-RAY DIFFRACTION | 99 | 2.4398-2.5926 | 0.2599 | 109 | 0.18 | 2607 | X-RAY DIFFRACTION | 98 | 2.5926-2.7928 | 0.23 | 149 | 0.1818 | 2579 | X-RAY DIFFRACTION | 98 | 2.7928-3.0737 | 0.2028 | 130 | 0.1894 | 2551 | X-RAY DIFFRACTION | 98 | 3.0737-3.5182 | 0.2333 | 153 | 0.1894 | 2577 | X-RAY DIFFRACTION | 97 | 3.5182-4.4314 | 0.1965 | 132 | 0.1647 | 2591 | X-RAY DIFFRACTION | 96 | 4.4314-37.547 | 0.2141 | 130 | 0.1718 | 2639 | X-RAY DIFFRACTION | 92 |
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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 | 0.669 | 0.1604 | 0.1519 | 0.3261 | -0.0386 | 0.1714 | 0.1403 | -0.0704 | -0.459 | 0.1444 | -0.2873 | 0.5188 | 0.1219 | -0.1137 | -0.0006 | 0.2984 | 0.0003 | 0.054 | 0.2884 | -0.0162 | 0.3987 | -17.6121 | 23.6324 | 60.2904 | 2 | 0.7238 | -0.4025 | 0.0857 | 1.0069 | -0.1338 | 0.2493 | 0.2254 | 0.1184 | 0.1233 | -0.2503 | -0.2175 | -0.2179 | -0.0296 | 0.055 | -0.0123 | 0.2256 | 0.0674 | 0.0755 | 0.186 | 0.0612 | 0.1963 | 11.0269 | 17.6402 | 54.4153 | 3 | 0.3065 | -0.3554 | -0.0181 | 0.8119 | -0.1711 | 0.5675 | 0.0654 | 0.0556 | 0.0732 | -0.0789 | -0.1013 | -0.1286 | 0.0706 | 0.1158 | 0.0001 | 0.184 | 0.0355 | 0.05 | 0.1481 | 0.0295 | 0.1736 | 10.4921 | 10.0947 | 62.646 | 4 | 0.5867 | -0.6078 | -0.0895 | 1.3267 | -0.4601 | 0.0094 | 0.1015 | -0.0667 | 0.0108 | -0.0716 | -0.1417 | -0.0751 | 0.1086 | -0.0266 | -0.0602 | 0.2597 | 0.1027 | 0.0421 | 0.1177 | 0.0258 | 0.1578 | 6.4847 | 18.0159 | 57.4276 |
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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 'A' and (resid 40 through 63 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 64 through 220 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 221 through 299 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 300 through 399 ) | | | |
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