ソフトウェア | 名称 | バージョン | 分類 |
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CNS | 1.1 | 精密化 | CrystalClear | (MSC/RIGAKU)データ削減 | CrystalClear | (MSC/RIGAKU)データスケーリング | MOLREP | | 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: PDB ENTRY 1VMH 解像度: 1.84→41.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1616402.7 / 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 | 0.239 | 1476 | 5.1 % | RANDOM |
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Rwork | 0.199 | - | - | - |
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all | 0.209 | 29020 | - | - |
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obs | 0.199 | 29019 | 99.8 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 43.3149 Å2 / ksol: 0.374358 e/Å3 |
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原子変位パラメータ | Biso mean: 21.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.26 Å | 0.2 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.15 Å | 0.14 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.84→41.17 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3016 | 0 | 0 | 224 | 3240 |
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拘束条件 | Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.005 | 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_deg1.3 | X-RAY DIFFRACTION | c_angle_deg_na | X-RAY DIFFRACTION | c_angle_deg_prot | X-RAY DIFFRACTION | c_dihedral_angle_d24.4 | X-RAY DIFFRACTION | c_dihedral_angle_d_na | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | X-RAY DIFFRACTION | c_improper_angle_d0.8 | X-RAY DIFFRACTION | c_improper_angle_d_na | X-RAY DIFFRACTION | c_improper_angle_d_prot | X-RAY DIFFRACTION | c_mcbond_it | X-RAY DIFFRACTION | c_mcangle_it | X-RAY DIFFRACTION | c_scbond_it | X-RAY DIFFRACTION | c_scangle_it | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.84→1.96 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.265 | 233 | 4.9 % |
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Rwork | 0.225 | 4569 | - |
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obs | - | 4731 | 100 % |
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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.top | | | |
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