ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1_4487精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.76→42.02 Å / SU ML: 0.2209 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 24.8915 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2019 | 1990 | 4.73 % |
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Rwork | 0.1711 | 40064 | - |
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obs | 0.1725 | 42054 | 98.53 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 38.92 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.76→42.02 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2790 | 0 | 1 | 200 | 2991 |
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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_d0.0073 | 2878 | X-RAY DIFFRACTION | f_angle_d0.9892 | 3893 | X-RAY DIFFRACTION | f_chiral_restr0.0512 | 419 | X-RAY DIFFRACTION | f_plane_restr0.008 | 500 | X-RAY DIFFRACTION | f_dihedral_angle_d5.8381 | 412 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.76-1.8 | 0.4391 | 125 | 0.3883 | 2744 | X-RAY DIFFRACTION | 95.67 | 1.8-1.85 | 0.3066 | 146 | 0.3242 | 2820 | X-RAY DIFFRACTION | 97.69 | 1.85-1.91 | 0.2613 | 130 | 0.2642 | 2820 | X-RAY DIFFRACTION | 97.91 | 1.91-1.97 | 0.2569 | 144 | 0.217 | 2825 | X-RAY DIFFRACTION | 97.92 | 1.97-2.04 | 0.2131 | 139 | 0.1942 | 2858 | X-RAY DIFFRACTION | 98.2 | 2.04-2.12 | 0.2117 | 142 | 0.1766 | 2832 | X-RAY DIFFRACTION | 98.54 | 2.12-2.22 | 0.22 | 141 | 0.1698 | 2856 | X-RAY DIFFRACTION | 98.75 | 2.22-2.33 | 0.1636 | 150 | 0.161 | 2868 | X-RAY DIFFRACTION | 98.98 | 2.33-2.48 | 0.2145 | 143 | 0.1614 | 2871 | X-RAY DIFFRACTION | 98.92 | 2.48-2.67 | 0.2362 | 139 | 0.1711 | 2867 | X-RAY DIFFRACTION | 99.21 | 2.67-2.94 | 0.1936 | 147 | 0.1719 | 2883 | X-RAY DIFFRACTION | 99.21 | 2.94-3.36 | 0.2025 | 143 | 0.1604 | 2907 | X-RAY DIFFRACTION | 99.22 | 3.36-4.24 | 0.1671 | 145 | 0.1475 | 2918 | X-RAY DIFFRACTION | 99.51 | 4.24-42.02 | 0.1895 | 156 | 0.1543 | 2995 | X-RAY DIFFRACTION | 99.62 |
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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 | 1.49834409258 | 0.269255801577 | 0.380722816631 | 2.09000660828 | -0.443600632285 | 1.93309002587 | -0.0257595349465 | -0.0662073030997 | -0.21711138242 | 0.0703725435904 | 0.0799197102247 | 0.152571499836 | 0.156053449798 | -0.0294430918756 | -0.0464738161226 | 0.214699007445 | 0.0401500496701 | 0.0291019068404 | 0.217741544285 | 0.00688427319083 | 0.259447811192 | -8.47892388576 | -32.065463428 | 15.1443016398 | 2 | 1.39954344217 | 0.0162330989161 | -0.0606640849471 | 1.74680838422 | 0.414146284725 | 2.76704429895 | 0.095859448267 | -0.0879852850114 | 0.0364926034758 | 0.0652080650884 | -0.175715870888 | 0.0142467650364 | -0.0831185808037 | 0.102298050218 | 0.0661694588913 | 0.233115700699 | -0.0362005340081 | -0.000475128771428 | 0.297926890095 | 0.0110390379707 | 0.245734037852 | -6.04832590979 | -26.9499336569 | 41.7976784607 | 3 | 2.80440990177 | -0.499369607203 | 0.173786181921 | 0.817139566401 | -0.12417859595 | 2.97368996948 | 0.0271654611247 | 0.274907468637 | -0.0275544108915 | -0.039074236533 | -0.0653175581425 | 0.0366374494712 | 0.0508123983742 | -0.102153753421 | 0.0339852463256 | 0.238156246669 | 0.0140033661828 | -0.00440583444336 | 0.237758717841 | -0.00706309945963 | 0.221918597326 | -16.3662879401 | -26.1690892822 | -8.87754653702 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | chain AAA6 - 134 | 1 - 116 | 2 | 2 | chain BBB2 - 128 | 1 - 127 | 3 | 3 | chain CCC2 - 119 | 1 - 118 | | | | | | | | | |
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