ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (phenix.refine: 1.9_1692)精密化 | PDB_EXTRACT | 3.15 | データ抽出 | XDS | | data processingAimless | | データスケーリング | PHASER | | 位相決定 | XDS | | データ削減 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5CO3 解像度: 1.801→31.935 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 18.92 / 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 | 1253 | 4.82 % |
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Rwork | 0.1625 | 24720 | - |
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obs | 0.1641 | 25973 | 99.78 % |
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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: 94.68 Å2 / Biso mean: 26.6387 Å2 / Biso min: 9.08 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.801→31.935 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1868 | 0 | 36 | 162 | 2066 |
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Biso mean | - | - | 42.96 | 35.91 | - |
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残基数 | - | - | - | - | 245 |
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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_d0.006 | 1943 | X-RAY DIFFRACTION | f_angle_d0.907 | 2628 | X-RAY DIFFRACTION | f_chiral_restr0.038 | 278 | X-RAY DIFFRACTION | f_plane_restr0.004 | 353 | X-RAY DIFFRACTION | f_dihedral_angle_d14.399 | 706 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8011-1.8732 | 0.2866 | 142 | 0.2432 | 2697 | 2839 | 100 | 1.8732-1.9584 | 0.2412 | 147 | 0.2026 | 2700 | 2847 | 100 | 1.9584-2.0616 | 0.2144 | 136 | 0.1783 | 2704 | 2840 | 100 | 2.0616-2.1908 | 0.1813 | 123 | 0.1588 | 2711 | 2834 | 100 | 2.1908-2.3599 | 0.1972 | 145 | 0.151 | 2732 | 2877 | 100 | 2.3599-2.5973 | 0.2091 | 124 | 0.1619 | 2747 | 2871 | 100 | 2.5973-2.9728 | 0.2026 | 148 | 0.1583 | 2740 | 2888 | 100 | 2.9728-3.7445 | 0.197 | 126 | 0.1483 | 2809 | 2935 | 100 | 3.7445-31.9396 | 0.1664 | 162 | 0.1578 | 2880 | 3042 | 99 |
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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 | 3.3651 | 0.1047 | -0.8712 | 1.0221 | 0.2622 | 2.257 | -0.0257 | -0.3726 | -0.5075 | 0.4379 | 0.014 | 0.2726 | 0.3685 | -0.0734 | 0.0372 | 0.3117 | -0.0231 | 0.0548 | 0.1707 | 0.0576 | 0.2975 | 1.8134 | 143.5125 | 107.9397 | 2 | 1.4837 | 0.1555 | 0.1945 | 1.1219 | -0.1696 | 0.4841 | -0.0456 | -0.1706 | -0.2054 | 0.2332 | 0.0219 | 0.1701 | 0.0354 | -0.0133 | 0.0224 | 0.1896 | 0.0037 | 0.027 | 0.1458 | 0.0314 | 0.1628 | -1.9595 | 151.7264 | 104.7833 | 3 | 0.1621 | -0.1274 | 0.2109 | 0.2778 | -0.6115 | 1.2634 | -0.057 | 0.3352 | -0.1956 | -0.2184 | -0.0361 | -0.1804 | 0.2842 | 0.3024 | 0.0511 | 0.2104 | 0.0124 | 0.0447 | 0.3007 | -0.0711 | 0.2306 | 19.3236 | 152.9807 | 89.0066 | 4 | 1.217 | 0.3223 | 0.0689 | 0.7201 | 0.0981 | 0.9376 | 0.0496 | 0.0719 | -0.0838 | -0.0421 | 0.0397 | -0.0119 | 0.0315 | -0.0033 | -0.0968 | 0.126 | -0.0014 | -0.003 | 0.1275 | 0.0121 | 0.1391 | 11.3206 | 158.4682 | 96.685 | 5 | 1.1918 | 0.3339 | 0.4163 | 0.6681 | -0.0857 | 1.2073 | 0.0676 | -0.1814 | -0.1309 | 0.1274 | -0.0316 | -0.0486 | -0.0498 | -0.0128 | -0.03 | 0.1435 | -0.0049 | -0.0257 | 0.1478 | 0.0173 | 0.1076 | 17.1048 | 160.1133 | 108.4662 | 6 | 2.266 | 2.1767 | 0.8469 | 2.9063 | 1.8129 | 1.5343 | 0.2389 | -0.2358 | -0.8738 | 0.2144 | -0.1276 | -0.2481 | 0.5295 | -0.0435 | 0.0024 | 0.2612 | 0.0261 | -0.0542 | 0.1222 | 0.059 | 0.431 | 16.2783 | 141.0749 | 106.5222 | 7 | 1.8895 | -0.2392 | -0.1894 | 1.4432 | 0.0976 | 1.7497 | -0.2052 | 0.4072 | -0.3202 | 0.0447 | 0.2322 | 0.0541 | 0.3139 | -0.3353 | -0.0246 | 0.2481 | -0.0521 | 0.0228 | 0.1432 | -0.0159 | 0.265 | 1.0155 | 142.3321 | 97.9441 | 8 | 2.8601 | 3.0654 | -1.3664 | 3.1443 | -1.5224 | 0.5258 | -0.0089 | 0.0626 | -0.5564 | 0.4676 | -0.1736 | -0.4293 | -0.1927 | -0.0004 | 0.1565 | 0.2681 | -0.0325 | 0.0272 | 0.215 | -0.0235 | 0.3482 | -16.0644 | 138.3684 | 107.238 | 9 | 2.6267 | 1.5755 | -1.9705 | 1.6222 | -0.0707 | 4.0263 | 0.5094 | 0.1813 | 0.1021 | -0.4614 | -0.0749 | -0.2595 | 0.0672 | 0.1346 | -0.2604 | 0.3089 | 0.0101 | -0.0117 | 0.2599 | 0.0611 | 0.2541 | -26.9859 | 116.2062 | 128.3521 |
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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 4 through 22 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 23 through 51 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 52 through 77 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 78 through 122 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 123 through 169 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 170 through 185 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 186 through 207 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 208 through 232 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 233 through 248 )A0 | | | | | | | | | | | | | | | | | | |
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