ソフトウェア | 名称 | バージョン | 分類 | NB |
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PHENIX | 1.9_1692精密化 | | XSCALE | | データスケーリング | | PDB_EXTRACT | 3.22 | データ抽出 | | |
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精密化 | 解像度: 1.697→42.618 Å / SU ML: 0.2 / σ(F): 1.33 / 位相誤差: 24.71 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2369 | 1803 | 5.01 % |
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Rwork | 0.1963 | 34212 | - |
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obs | 0.1984 | 36015 | 97.06 % |
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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: 62.57 Å2 / Biso mean: 20.7789 Å2 / Biso min: 6.86 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.697→42.618 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2389 | 0 | 60 | 264 | 2713 |
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Biso mean | - | - | 31.41 | 27.03 | - |
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残基数 | - | - | - | - | 330 |
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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 | 2585 | X-RAY DIFFRACTION | f_angle_d1.05 | 3552 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 417 | X-RAY DIFFRACTION | f_plane_restr0.005 | 474 | X-RAY DIFFRACTION | f_dihedral_angle_d10.555 | 892 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6968-1.7426 | 0.3258 | 135 | 0.2693 | 2558 | 2693 | 94 | 1.7426-1.7939 | 0.2877 | 139 | 0.2582 | 2649 | 2788 | 99 | 1.7939-1.8518 | 0.2912 | 143 | 0.2562 | 2707 | 2850 | 100 | 1.8518-1.918 | 0.3943 | 126 | 0.3257 | 2379 | 2505 | 88 | 1.918-1.9948 | 0.3294 | 133 | 0.2618 | 2517 | 2650 | 93 | 1.9948-2.0856 | 0.2129 | 141 | 0.1992 | 2678 | 2819 | 100 | 2.0856-2.1955 | 0.2239 | 141 | 0.1841 | 2689 | 2830 | 100 | 2.1955-2.3331 | 0.3572 | 128 | 0.2954 | 2427 | 2555 | 90 | 2.3331-2.5132 | 0.2396 | 143 | 0.1961 | 2713 | 2856 | 100 | 2.5132-2.7661 | 0.2361 | 142 | 0.1832 | 2703 | 2845 | 100 | 2.7661-3.1662 | 0.2415 | 144 | 0.1763 | 2722 | 2866 | 100 | 3.1662-3.9886 | 0.1818 | 142 | 0.1711 | 2709 | 2851 | 99 | 3.9886-42.6316 | 0.1678 | 146 | 0.1284 | 2761 | 2907 | 100 |
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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 | 0.4627 | -0.0597 | 0.0307 | 0.5133 | -0.1193 | 0.0989 | -0.0603 | 0.0445 | 0.0527 | 0.2739 | 0.0696 | 0.0344 | -0.0589 | -0.0303 | -0.0014 | 0.1627 | 0.0161 | 0.0256 | 0.0929 | 0.0058 | 0.0953 | 0.2001 | -8.4934 | 14.3965 | 2 | 0.1188 | 0.0214 | -0.0951 | 0.0132 | 0.0074 | 0.0965 | 0.0731 | 0.0284 | 0.0298 | -0.1161 | -0.0507 | 0.0277 | -0.0431 | -0.0024 | 0.1166 | 0.507 | 0.0703 | -0.0211 | 0.1501 | -0.0023 | 0.0916 | 2.9603 | -1.9647 | 25.0208 | 3 | 0.3744 | -0.0827 | -0.1603 | 0.3979 | -0.1353 | 0.2129 | -0.0995 | -0.0335 | 0.0283 | 0.5059 | 0.0283 | -0.1114 | -0.2532 | 0.0108 | -0.0977 | 0.3151 | 0.0206 | -0.0692 | 0.1163 | -0.0004 | 0.1065 | 5.7808 | -2.392 | 18.8618 | 4 | 0.0631 | 0.1253 | -0.1126 | 0.26 | -0.2506 | 0.186 | -0.0275 | 0.0886 | -0.0332 | 0.0027 | -0.0123 | -0.1219 | -0.0149 | 0.0573 | -0.0006 | 0.082 | 0.0038 | -0.0205 | 0.1244 | 0.0064 | 0.169 | 14.6952 | -3.9116 | -0.4456 | 5 | 0.0573 | -0.1125 | 0.0223 | 0.3272 | -0.0844 | 0.0239 | 0.0114 | 0.0733 | 0.1395 | 0.1333 | -0.0323 | -0.2439 | -0.0663 | -0.1879 | 0.0142 | 0.1077 | -0.008 | -0.0078 | 0.1379 | 0.01 | 0.1699 | 10.2108 | 12.1595 | 0.0898 | 6 | 0.1027 | -0.03 | 0.0179 | 0.1088 | 0.0458 | 0.0286 | -0.0101 | 0.0071 | 0.0494 | 0.0011 | -0.0032 | -0.0194 | 0.0023 | -0.0083 | 0 | 0.0957 | -0.0033 | 0.0117 | 0.1007 | 0.0189 | 0.0762 | 0.7487 | 12.2539 | -7.5124 | 7 | 0.0095 | -0.0129 | 0.0127 | 0.0896 | -0.0333 | 0.0348 | -0.1192 | 0.1007 | 0.09 | 0.035 | 0.1306 | 0.2613 | -0.0107 | -0.037 | -0.0112 | 0.0784 | -0.025 | 0.0445 | 0.1619 | -0.0105 | 0.1522 | -13.6963 | 9.5344 | -8.1826 | 8 | 0.1144 | -0.1318 | 0.0171 | 0.5191 | -0.1557 | 0.2882 | 0.0096 | 0.0029 | 0.0245 | 0.0358 | -0.0567 | -0.0633 | -0.0448 | 0.0213 | -0.0355 | 0.0591 | -0.0129 | 0.0104 | 0.0987 | 0.0001 | 0.0936 | 2.9871 | 4.9734 | -4.3951 |
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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 1:62)A1 - 62 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 63:81)A63 - 81 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 82:151)A82 - 151 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 152:190)A152 - 190 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 191:204)A191 - 204 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 205:242)A205 - 242 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 243:258)A243 - 258 | 8 | X-RAY DIFFRACTION | 8 | (chain A and resid 259:330)A259 - 330 | | | | | | | | | | | | | | | | |
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