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 | MOSFLM | | データ削減 | CCP4 | (SCALA)データスケーリング | AMoRE | | 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 1NE9 解像度: 2→14.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1126187.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 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 | 0.214 | 1254 | 5 % | RANDOM |
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Rwork | 0.175 | - | - | - |
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all | 0.193 | 25933 | - | - |
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obs | 0.175 | 25104 | 97.1 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 60.6839 Å2 / ksol: 0.402607 e/Å3 |
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原子変位パラメータ | Biso mean: 20.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.94 Å2 | 0 Å2 | 4.72 Å2 |
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2- | - | -5.59 Å2 | 0 Å2 |
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3- | - | - | 9.53 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.23 Å | 0.19 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.2 Å | 0.16 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2→14.97 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2688 | 0 | 0 | 487 | 3175 |
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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_d0.005 | | 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_deg1.2 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d23.1 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d0.74 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.27 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.96 | 2 | X-RAY DIFFRACTION | c_scbond_it2.09 | 2 | X-RAY DIFFRACTION | c_scangle_it3.04 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.259 | 214 | 5.1 % |
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Rwork | 0.217 | 4017 | - |
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obs | - | 4017 | 97.8 % |
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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.TOP | | | | | |
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