ソフトウェア | 名称 | バージョン | 分類 |
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MxCuBE | | データ収集 | XDS | | データ削減 | XDS | | データスケーリング | Coot | | モデル構築 | PHASER | 1.19.2_4158位相決定 | PHENIX | 1.19.2_4158精密化 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 7NCZ 解像度: 1.46→40.45 Å / SU ML: 0.207 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.4337 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 | 0.1986 | 2037 | 5 % |
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Rwork | 0.1767 | 38686 | - |
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obs | 0.1779 | 40723 | 99.45 % |
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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 mean: 34.88 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.46→40.45 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1742 | 0 | 73 | 191 | 2006 |
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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_d0.0084 | 1904 | X-RAY DIFFRACTION | f_angle_d1.3778 | 2609 | X-RAY DIFFRACTION | f_chiral_restr0.1201 | 327 | X-RAY DIFFRACTION | f_plane_restr0.0073 | 331 | X-RAY DIFFRACTION | f_dihedral_angle_d18.7422 | 641 | | | | | |
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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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1.46-1.49 | 0.4438 | 125 | 0.4312 | 2357 | X-RAY DIFFRACTION | 92.44 | 1.49-1.53 | 0.3744 | 133 | 0.3523 | 2557 | X-RAY DIFFRACTION | 99.81 | 1.53-1.57 | 0.3236 | 134 | 0.3076 | 2532 | X-RAY DIFFRACTION | 99.89 | 1.57-1.62 | 0.2912 | 135 | 0.2627 | 2563 | X-RAY DIFFRACTION | 100 | 1.62-1.67 | 0.2875 | 135 | 0.2541 | 2579 | X-RAY DIFFRACTION | 99.93 | 1.67-1.73 | 0.3012 | 135 | 0.2489 | 2560 | X-RAY DIFFRACTION | 100 | 1.73-1.8 | 0.2641 | 135 | 0.2209 | 2548 | X-RAY DIFFRACTION | 99.93 | 1.8-1.88 | 0.2269 | 135 | 0.1904 | 2563 | X-RAY DIFFRACTION | 99.93 | 1.88-1.98 | 0.1769 | 135 | 0.1777 | 2579 | X-RAY DIFFRACTION | 99.93 | 1.98-2.1 | 0.2005 | 136 | 0.1743 | 2588 | X-RAY DIFFRACTION | 100 | 2.1-2.26 | 0.2022 | 137 | 0.1658 | 2598 | X-RAY DIFFRACTION | 99.93 | 2.26-2.49 | 0.2034 | 138 | 0.1673 | 2609 | X-RAY DIFFRACTION | 99.96 | 2.49-2.85 | 0.2104 | 137 | 0.1714 | 2607 | X-RAY DIFFRACTION | 100 | 2.85-3.59 | 0.1739 | 139 | 0.1669 | 2652 | X-RAY DIFFRACTION | 99.96 | 3.59-40.45 | 0.1674 | 148 | 0.1514 | 2794 | X-RAY DIFFRACTION | 99.93 |
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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 | 8.12273607669 | -0.770033761811 | 0.954062237935 | 3.09605346027 | -1.7945493877 | 4.820300125 | -0.077437925166 | 0.0297066440206 | 0.0432296814467 | -0.272742073977 | 0.10061586866 | -0.271235829978 | 0.286921387078 | 0.278959717101 | -0.0345431158038 | 0.255991214695 | 0.0246306199819 | 0.0149021665503 | 0.169748240433 | -0.0526298212118 | 0.174129165572 | 4.4460252337 | 12.7527148113 | 5.14217123689 | 2 | 1.49434043795 | 0.532744989548 | 0.707450767948 | 2.8814032094 | 0.720603342347 | 2.85870665308 | 0.018519068856 | -0.194346210722 | 0.0435674504901 | 0.226285773636 | -0.00438839393791 | -0.0751220669917 | 0.0074552735881 | -0.11717614947 | 0.00476814957089 | 0.195267301607 | 0.00367442893927 | -0.0261086735136 | 0.210048270392 | -0.0067758717604 | 0.190165498458 | 1.72557739415 | 22.4645138713 | 21.0984531118 | 3 | 4.75445838024 | 0.83803285219 | 0.579710255544 | 3.03091990159 | 1.34543346806 | 3.38324121333 | -0.0313750061848 | 0.00658615780614 | 0.189564456889 | 0.241824593936 | 0.0540512325161 | -0.308162055476 | -0.325826412634 | 0.238698860226 | -0.0392327605151 | 0.351900466566 | -0.0373338567872 | -0.0603970807761 | 0.189106182101 | -0.00776842180002 | 0.243842149439 | 2.40675687433 | 20.5597776778 | 16.7401539501 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A ID | Refine TLS-ID | Selection details | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 0 through 63 )0 - 63 | 2 - 43 | 2 | 2 | chain 'A' and (resid 64 through 232 )64 - 232 | 44 - 212 | 3 | 3 | chain 'A' and (resid 233 through 248 )233 - 247 | 213 - 227 | | | |
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