ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | Aimless | 0.7.4データスケーリング | PHENIX | 1.19rc5精密化 | PDB_EXTRACT | 3.27 | データ抽出 | AutoSol | | 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: 2.01→57.49 Å / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 20.83 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1952 | 1321 | 4.85 % |
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Rwork | 0.1646 | 25911 | - |
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obs | 0.1661 | 27232 | 99.93 % |
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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: 144.49 Å2 / Biso mean: 48.4788 Å2 / Biso min: 23.92 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.01→57.49 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3001 | 0 | 30 | 168 | 3199 |
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Biso mean | - | - | 65.25 | 43.45 | - |
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残基数 | - | - | - | - | 381 |
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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: 9 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.01-2.09 | 0.2684 | 139 | 0.2409 | 2883 | 3022 | 2.09-2.19 | 0.2501 | 176 | 0.206 | 2816 | 2992 | 2.19-2.3 | 0.229 | 152 | 0.1863 | 2839 | 2991 | 2.3-2.45 | 0.2249 | 178 | 0.1816 | 2830 | 3008 | 2.45-2.63 | 0.2264 | 154 | 0.1739 | 2864 | 3018 | 2.63-2.9 | 0.2088 | 93 | 0.1623 | 2922 | 3015 | 2.9-3.32 | 0.1878 | 110 | 0.1702 | 2913 | 3023 | 3.32-4.18 | 0.177 | 161 | 0.1435 | 2902 | 3063 | 4.18-57.49 | 0.1675 | 158 | 0.1533 | 2942 | 3100 |
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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 | 1.7979 | 0.1616 | 1.5691 | 0.7386 | -0.3784 | 5.9804 | 0.0339 | 0.5541 | 0.0193 | -0.2161 | 0.1391 | -0.0048 | 0.2458 | -0.5541 | -0.1616 | 0.3277 | -0.0207 | -0.0352 | 0.5565 | -0.0142 | 0.3107 | -3.481 | 13.4852 | 9.2453 | 2 | 3.7417 | -0.4616 | 0.0031 | 0.2115 | 0.0498 | 0.6163 | 0.0104 | -0.5546 | -0.0801 | 0.0524 | 0.0072 | 0.0008 | 0.021 | -0.121 | -0.0374 | 0.3256 | -0.0362 | 0.0185 | 0.3039 | 0.0169 | 0.3124 | 16.4159 | 13.2291 | 38.3494 | 3 | 3.867 | 1.3996 | -1.0779 | 2.7875 | -1.3993 | 2.6201 | -0.0373 | 0.4293 | 0.587 | -0.067 | -0.095 | 0.0539 | -0.1894 | -0.2967 | 0.1307 | 0.3377 | 0.0646 | -0.0432 | 0.3119 | 0.0228 | 0.4085 | 0.6248 | 27.6672 | 18.863 | 4 | 3.093 | -0.0713 | 0.9654 | 1.0965 | -0.0178 | 2.2358 | 0.1073 | 1.166 | 0.3713 | -0.2389 | -0.1747 | -0.0295 | -0.0413 | 0.0856 | 0.0245 | 0.293 | 0.078 | 0.023 | 0.5199 | 0.0998 | 0.2497 | 17.1251 | 19.4867 | 9.3233 | 5 | 3.5893 | -1.7776 | -0.4656 | 3.4822 | 0.9899 | 2.049 | 0.0947 | 0.3536 | 0.0751 | -0.0971 | -0.1034 | 0.144 | -0.0965 | -0.0891 | 0.0197 | 0.2677 | 0.0227 | -0.0086 | 0.2956 | 0.0301 | 0.2581 | 4.0488 | 20.5333 | 21.208 | 6 | 6.1342 | 0.0513 | 0.2602 | 0.1077 | 0.0096 | 4.5112 | 0.0433 | 0.2142 | -0.2004 | -0.2047 | -0.0355 | -0.0618 | -0.0661 | -0.2858 | 0.0088 | 0.2631 | -0.0032 | -0.0092 | 0.2479 | 0.0193 | 0.2514 | 17.2053 | 11.6642 | 24.7084 | 7 | 4.4467 | -0.0734 | -0.2938 | 4.0854 | 1.1375 | 3.5857 | 0.0906 | -0.2845 | 0.6996 | 0.1541 | -0.0858 | 0.1416 | -0.4011 | -0.3235 | 0.0352 | 0.3027 | -0.0315 | 0.0231 | 0.2941 | -0.0325 | 0.3848 | 15.3215 | 21.6275 | 37.8315 | 8 | 2.0468 | -0.2601 | 0.5638 | 1.5111 | -0.6067 | 1.3406 | 0.0269 | 0.8614 | 0.6237 | -0.2186 | -0.1473 | -0.2251 | -0.1404 | 0.1704 | 0.063 | 0.2933 | 0.0317 | 0.0535 | 0.4498 | 0.2043 | 0.4335 | 25.5705 | 24.782 | 14.4146 |
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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 5 through 25 )A5 - 25 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 26 through 86 )A26 - 86 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 87 through 123 )A87 - 123 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 124 through 198 )A124 - 198 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 199 through 244 )A199 - 244 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 245 through 292 )A245 - 292 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 293 through 327 )A293 - 327 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 328 through 391 )A328 - 391 | | | | | | | | | | | | | | | | |
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