ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHENIX | (phenix.refine: 1.8.2_1309)精密化 | | PDB_EXTRACT | 3.15 | データ抽出 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | HKL-2000 | | データスケーリング | | SOLVE | | 位相決定 | | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 1.9→33.74 Å / FOM work R set: 0.8505 / SU ML: 0.21 / σ(F): 1.34 / 位相誤差: 22.83 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2264 | 1991 | 4.24 % |
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Rwork | 0.1951 | - | - |
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obs | 0.1964 | 47009 | 99.59 % |
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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: 81.13 Å2 / Biso mean: 30.26 Å2 / Biso min: 11.62 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→33.74 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3978 | 0 | 0 | 358 | 4336 |
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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 | 4048 | X-RAY DIFFRACTION | f_angle_d1.096 | 5456 | X-RAY DIFFRACTION | f_chiral_restr0.071 | 590 | X-RAY DIFFRACTION | f_plane_restr0.004 | 726 | X-RAY DIFFRACTION | f_dihedral_angle_d14.89 | 1574 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8996-1.9471 | 0.2726 | 142 | 0.2585 | 3194 | 3336 | 99 | 1.9471-1.9997 | 0.2673 | 141 | 0.2556 | 3241 | 3382 | 100 | 1.9997-2.0586 | 0.2746 | 144 | 0.2236 | 3196 | 3340 | 100 | 2.0586-2.125 | 0.2741 | 135 | 0.2189 | 3213 | 3348 | 100 | 2.125-2.2009 | 0.2483 | 140 | 0.2126 | 3245 | 3385 | 100 | 2.2009-2.289 | 0.258 | 143 | 0.2134 | 3204 | 3347 | 100 | 2.289-2.3932 | 0.2577 | 144 | 0.2102 | 3236 | 3380 | 100 | 2.3932-2.5193 | 0.267 | 149 | 0.2153 | 3216 | 3365 | 100 | 2.5193-2.6771 | 0.2277 | 143 | 0.2042 | 3216 | 3359 | 100 | 2.6771-2.8837 | 0.2247 | 142 | 0.2009 | 3215 | 3357 | 100 | 2.8837-3.1737 | 0.22 | 140 | 0.1903 | 3265 | 3405 | 100 | 3.1737-3.6325 | 0.181 | 141 | 0.1737 | 3209 | 3350 | 100 | 3.6325-4.5747 | 0.1979 | 143 | 0.1632 | 3207 | 3350 | 99 | 4.5747-33.7451 | 0.2302 | 144 | 0.1975 | 3161 | 3305 | 97 |
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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 | 0.7766 | 0.5182 | 0.4685 | 1.6408 | 0.6719 | 0.455 | -0.112 | 0.0948 | -0.1149 | -0.2894 | 0.0791 | -0.128 | -0.0893 | 0.1193 | -0.0292 | 0.2235 | -0.0096 | 0.0604 | 0.1542 | 0.0047 | 0.1239 | 4.8827 | -20.9769 | -4.2758 | 2 | 1.2644 | -0.1756 | -0.1977 | 0.4433 | -0.0096 | 0.1481 | -0.0945 | 0.0671 | 0.2505 | -0.4056 | 0.0167 | -0.1827 | -0.1 | 0.0729 | 0.029 | 0.3176 | -0.0349 | 0.0237 | 0.1513 | 0.0313 | 0.2025 | 6.9897 | -9.1589 | -5.173 | 3 | 0.9032 | 0.3063 | -0.2435 | 0.7253 | 0.1524 | 1.1316 | -0.0884 | -0.1995 | 0.161 | 0.0119 | -0.068 | 0.1764 | -0.0778 | 0.0137 | -0.2942 | 0.1905 | 0.0032 | -0.0053 | 0.1508 | -0.0571 | 0.1877 | -5.4301 | -12.3591 | 8.1202 | 4 | 0.3173 | 0.0386 | -0.0949 | 0.297 | -0.0099 | 0.234 | 0.0841 | 0.0354 | -0.0147 | -0.0858 | -0.0221 | -0.2071 | -0.1413 | -0.0421 | 0.011 | 0.1744 | 0.0213 | -0.0476 | 0.1711 | 0.0207 | 0.2229 | 8.1005 | -36.3464 | 1.7085 | 5 | 0.4216 | 0.1806 | -0.1232 | 0.4825 | 0.0436 | 0.589 | 0.1109 | 0.0951 | 0.0206 | -0.2582 | -0.2355 | 0.4336 | -0.1665 | -0.1288 | 0.014 | 0.2357 | 0.0511 | -0.0812 | 0.1888 | -0.0601 | 0.2403 | -17.7527 | -33.6327 | -8.2669 | 6 | 0.4556 | -0.1062 | 0.0789 | 0.3007 | 0.0751 | 0.3572 | 0.0975 | 0.0387 | -0.1628 | -0.0823 | -0.1136 | 0.1649 | -0.0187 | -0.0471 | -0.0067 | 0.175 | -0.0099 | -0.0452 | 0.1041 | -0.0297 | 0.176 | -8.5915 | -46.5633 | -4.56 | 7 | 0.5105 | 0.2509 | -0.4435 | 0.3432 | -0.1793 | 0.4015 | 0.0661 | -0.1382 | -0.109 | 0.1096 | -0.1144 | -0.0731 | -0.0719 | -0.0731 | -0 | 0.2256 | -0.01 | -0.0431 | 0.1761 | 0.0345 | 0.2101 | 4.6017 | -43.2713 | 8.1711 |
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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 120 through 219 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain A and (resid 220 through 298 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain A and (resid 299 through 374 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain B and (resid 120 through 163 )B0 | 5 | X-RAY DIFFRACTION | 5 | chain B and (resid 164 through 219 )B0 | 6 | X-RAY DIFFRACTION | 6 | chain B and (resid 220 through 298 )B0 | 7 | X-RAY DIFFRACTION | 7 | chain B and (resid 299 through 374 )B0 | | | | | | | | | | | | | | |
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