ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データスケーリング | PHENIX | 1.9_1692精密化 | PDB_EXTRACT | 3.15 | データ抽出 | HKL-2000 | | データ削減 | PHASER | | 位相決定 | |
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精密化 | 解像度: 1.28→28.817 Å / SU ML: 0.1 / 交差検証法: FREE R-VALUE / σ(F): 1.43 / 位相誤差: 17.91 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1871 | 1663 | 4.97 % |
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Rwork | 0.1622 | 31808 | - |
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obs | 0.1634 | 33471 | 94.61 % |
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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: 76.04 Å2 / Biso mean: 20.0085 Å2 / Biso min: 5.4 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.28→28.817 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1163 | 0 | 43 | 241 | 1447 |
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Biso mean | - | - | 29.9 | 31.55 | - |
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残基数 | - | - | - | - | 154 |
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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 | 1249 | X-RAY DIFFRACTION | f_angle_d1.148 | 1683 | X-RAY DIFFRACTION | f_chiral_restr0.045 | 185 | X-RAY DIFFRACTION | f_plane_restr0.004 | 223 | X-RAY DIFFRACTION | f_dihedral_angle_d13 | 458 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.2802-1.3179 | 0.2139 | 136 | 0.191 | 2378 | 2514 | 85 | 1.3179-1.3604 | 0.2061 | 141 | 0.1828 | 2607 | 2748 | 94 | 1.3604-1.409 | 0.207 | 143 | 0.1797 | 2631 | 2774 | 95 | 1.409-1.4654 | 0.1891 | 132 | 0.1746 | 2646 | 2778 | 95 | 1.4654-1.5321 | 0.2072 | 129 | 0.1663 | 2682 | 2811 | 96 | 1.5321-1.6129 | 0.1774 | 147 | 0.1614 | 2681 | 2828 | 96 | 1.6129-1.7139 | 0.1788 | 145 | 0.1601 | 2701 | 2846 | 96 | 1.7139-1.8463 | 0.193 | 127 | 0.1632 | 2706 | 2833 | 97 | 1.8463-2.032 | 0.1624 | 129 | 0.1581 | 2747 | 2876 | 97 | 2.032-2.3259 | 0.1926 | 151 | 0.1515 | 2751 | 2902 | 98 | 2.3259-2.93 | 0.1772 | 169 | 0.1682 | 2748 | 2917 | 99 | 2.93-28.8244 | 0.1969 | 114 | 0.1567 | 2530 | 2644 | 88 |
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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 | 0.9176 | -0.07 | -0.3216 | 0.9319 | 0.251 | 2.5703 | -0.0663 | -0.1151 | -0.0537 | 0.1668 | -0.0236 | 0.1107 | 0.1943 | -0.4162 | 0.0555 | 0.109 | -0.0251 | 0.0163 | 0.1374 | -0.0087 | 0.108 | -10.9275 | 6.4338 | -6.7838 | 2 | 1.2531 | -1.8911 | -1.8908 | 3.2305 | 3.1365 | 3.4056 | 0.0559 | -0.1577 | 0.1681 | 0.2177 | 0.2185 | -0.3197 | 0.2188 | 0.3721 | -0.2898 | 0.0822 | -0.0075 | -0.0189 | 0.1084 | -0.0031 | 0.0987 | 4.5302 | 9.4127 | -16.5999 | 3 | 6.0988 | 3.3478 | -1.8788 | 3.1568 | -1.2614 | 2.3725 | -0.1676 | -0.1012 | -0.2635 | 0.0252 | -0.0237 | -0.0829 | 0.3312 | -0.1521 | 0.1913 | 0.1668 | -0.0208 | 0.0364 | 0.0712 | -0.0176 | 0.1148 | -7.1344 | -3.8274 | -14.5645 | 4 | 3.6871 | -1.2636 | -3.6275 | 5.0571 | 3.3204 | 7.6402 | -0.244 | 0.1216 | -0.2307 | -0.0112 | -0.0311 | -0.1466 | 0.5114 | -0.1261 | 0.3031 | 0.1378 | 0.0029 | 0.0002 | 0.0654 | 0.0073 | 0.0958 | -5.4761 | -1.9665 | -5.6177 | 5 | 8.1277 | -7.1443 | -5.8777 | 7.1265 | 5.0914 | 6.1057 | -0.2173 | -0.1067 | -0.202 | 0.071 | 0.1172 | -0.1823 | 0.5224 | 0.2571 | 0.0875 | 0.1824 | 0.0139 | 0.0237 | 0.0787 | -0.0129 | 0.139 | -1.9762 | -4.4227 | -6.447 | 6 | 2.0938 | -0.2308 | 0.309 | 1.2697 | -0.2035 | 3.3877 | -0.0731 | 0.0588 | -0.0132 | 0.0612 | 0.0154 | 0.0296 | 0.087 | -0.2074 | 0.051 | 0.0588 | -0.0129 | 0.0032 | 0.0606 | -0.0095 | 0.0542 | -8.6772 | 6.645 | -8.4684 | 7 | 3.7958 | -0.1967 | 0.9778 | 2.7118 | -0.5507 | 3.8789 | -0.008 | -0.1459 | -0.1626 | 0.2518 | 0.0616 | -0.2675 | -0.0777 | 0.486 | 0.0173 | 0.0723 | 0.0093 | -0.0177 | 0.1044 | -0.0006 | 0.0983 | 0.5937 | 8.0834 | -6.2817 | 8 | 0.6096 | -1.4832 | -1.2382 | 8.3014 | 1.3472 | 5.2924 | 0.0696 | 0.194 | 0.0815 | -0.4275 | 0.0878 | -0.1394 | -0.2706 | -0.3671 | -0.1398 | 0.0609 | 0.0237 | -0.019 | 0.1375 | -0.0085 | 0.0676 | -10.2999 | 11.2098 | -22.9123 | 9 | 4.0464 | 1.4008 | 4.6136 | 6.4759 | 1.1712 | 5.2768 | -0.1108 | -0.3817 | 0.2556 | 0.5721 | 0.0176 | 0.0336 | -0.2325 | -0.2322 | 0.1368 | 0.1888 | 0.0534 | 0.0077 | 0.1361 | -0.0005 | 0.1314 | -12.1223 | 21.9274 | -11.2824 | 10 | 3.2186 | -1.8837 | -3.8914 | 2.7211 | 1.8274 | 5.3291 | 0.1968 | -0.0876 | 0.2271 | -0.1002 | 0.2026 | -0.3558 | -0.7237 | 0.1651 | -0.3238 | 0.1821 | 0.0044 | -0.0048 | 0.0792 | 0.0069 | 0.1109 | -2.3669 | 16.3402 | -16.3044 |
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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 3 through 36 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 37 through 45 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 46 through 60 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 61 through 77 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 78 through 89 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 90 through 112 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 113 through 127 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 128 through 135 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 136 through 144 )A0 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 145 through 156 )A0 | | | | | | | | | | | | | | | | | | | | |
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