ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | PHASER | 2.5.6位相決定 | PHENIX | | 精密化 | PDB_EXTRACT | 3.22 | データ抽出 | 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: 1tro 解像度: 1.832→34.969 Å / SU ML: 0.23 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.92
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2167 | 1021 | 5 % |
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Rwork | 0.1773 | - | - |
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obs | 0.1792 | 20417 | 99.52 % |
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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 |
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原子変位パラメータ | Biso max: 110.12 Å2 / Biso mean: 36.0587 Å2 / Biso min: 15.1 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.832→34.969 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1701 | 0 | 26 | 155 | 1882 |
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Biso mean | - | - | 31.31 | 42.35 | - |
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残基数 | - | - | - | - | 209 |
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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_d0.013 | 1757 | X-RAY DIFFRACTION | f_angle_d1.202 | 2375 | X-RAY DIFFRACTION | f_chiral_restr0.076 | 261 | X-RAY DIFFRACTION | f_plane_restr0.009 | 309 | X-RAY DIFFRACTION | f_dihedral_angle_d6.202 | 1069 | | | | | |
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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: 7 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8322-1.9288 | 0.3645 | 140 | 0.3351 | 2673 | 2813 | 97 | 1.9288-2.0496 | 0.2821 | 143 | 0.2395 | 2722 | 2865 | 100 | 2.0496-2.2078 | 0.257 | 146 | 0.1853 | 2757 | 2903 | 100 | 2.2078-2.43 | 0.2214 | 144 | 0.1674 | 2745 | 2889 | 100 | 2.43-2.7814 | 0.2319 | 146 | 0.181 | 2764 | 2910 | 100 | 2.7814-3.5038 | 0.2079 | 147 | 0.1778 | 2805 | 2952 | 100 | 3.5038-34.9755 | 0.1847 | 155 | 0.1533 | 2930 | 3085 | 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 | 4.4374 | -0.6353 | 5.2032 | 0.0605 | -0.6406 | 5.5174 | -0.0288 | 0.2987 | 0.2998 | 0.0492 | -0.0735 | -0.2654 | 0.0716 | 0.2896 | -0.1508 | 0.2302 | 0.0174 | -0.012 | 0.2274 | 0.0045 | 0.2331 | 54.0921 | 12.525 | 41.3921 | 2 | 0.8211 | 0.1912 | 0.2905 | 5.9715 | 1.1912 | 2.1667 | 0.0085 | -0.0052 | 0.2423 | 0.1938 | -0.0262 | 0.3351 | -0.1948 | -0.0355 | 0.0454 | 0.1553 | 0.0187 | 0.0019 | 0.2194 | -0.0084 | 0.2063 | 39.0102 | 29.4917 | 41.856 | 3 | 6.4561 | -0.9677 | -6.8919 | 0.0235 | 0.5241 | 6.7103 | 0.0083 | 0.2794 | 0.2281 | 0.0511 | 0.0317 | 0.2101 | -0.0321 | -0.2517 | -0.0606 | 0.2295 | 0.0068 | 0.0029 | 0.2229 | -0.0269 | 0.2582 | 28.7062 | 23.0716 | 39.0647 | 4 | 0.9421 | 0.3883 | -0.5277 | 4.7101 | -3.133 | 3.6125 | 0.0807 | -0.1775 | -0.135 | 0.274 | -0.285 | -0.2672 | 0.0286 | 0.2435 | 0.2947 | 0.1849 | -0.0022 | -0.0223 | 0.2788 | 0.0209 | 0.1905 | 47.3069 | 9.0951 | 45.1227 | 5 | 4.43 | -0.1081 | -1.0038 | 3.5652 | -1.5844 | 2.0229 | -0.0431 | 0.3554 | -0.1774 | -0.1702 | 0.1653 | 0.2505 | 0.6062 | -0.4933 | -0.0571 | 0.1823 | -0.0158 | -0.0073 | 0.1889 | 0.0069 | 0.1844 | 37.6176 | 1.1764 | 40.9307 |
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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 'B' and (resid 2 through 31 )B2 - 31 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 32 through 105 )B32 - 105 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 2 through 31 )A2 - 31 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 32 through 78 )A32 - 78 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 79 through 106 )A79 - 106 | | | | | | | | | | |
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