ソフトウェア | 名称 | バージョン | 分類 |
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CrystalClear | | データ収集 | CNX | 2005 | 精密化 | CrystalClear | | データ削減 | CrystalClear | | データスケーリング | CNX | 2005 | 位相決定 |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1x3k 解像度: 1.81→33.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 446250.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.218 | 1575 | 10.1 % | RANDOM |
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Rwork | 0.187 | - | - | - |
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obs | 0.19 | 15586 | 99.3 % | - |
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all | - | 15653 | - | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 43.0386 Å2 / ksol: 0.38807 e/Å3 |
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原子変位パラメータ | Biso mean: 18.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.38 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.84 Å2 | 0 Å2 |
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3- | - | - | -1.22 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.22 Å | 0.18 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.15 Å | 0.08 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.81→33.53 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1213 | 0 | 48 | 299 | 1560 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.019 | | X-RAY DIFFRACTION | c_bond_d_na | | X-RAY DIFFRACTION | c_bond_d_prot | | X-RAY DIFFRACTION | c_angle_d | | X-RAY DIFFRACTION | c_angle_d_na | | X-RAY DIFFRACTION | c_angle_d_prot | | X-RAY DIFFRACTION | c_angle_deg1.7 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d18.8 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.81 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.52 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.32 | 2 | X-RAY DIFFRACTION | c_scbond_it2.74 | 2 | X-RAY DIFFRACTION | c_scangle_it4.03 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.81→1.92 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.276 | 252 | 9.9 % |
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Rwork | 0.221 | 2296 | - |
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obs | - | - | 99.9 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | water_rep.paramwater.topX-RAY DIFFRACTION | 3 | ion.paramion.topX-RAY DIFFRACTION | 4 | PaV-heme.param | PaV-heme.top | | | | | | |
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