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 | HKL-2000 | | データ削減 | SCALEPACK | | 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 1NB9 解像度: 2.42→35.15 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1023651.21 / 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 | 0.26 | 330 | 4.8 % | RANDOM |
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Rwork | 0.199 | - | - | - |
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all | 0.222 | 6905 | - | - |
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obs | 0.199 | 6896 | 99.7 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 42.0074 Å2 / ksol: 0.380922 e/Å3 |
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原子変位パラメータ | Biso mean: 32.2 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -5.92 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 4.07 Å2 | 0 Å2 |
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3- | - | - | 1.85 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.36 Å | 0.26 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.35 Å | 0.24 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.42→35.15 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1192 | 0 | 59 | 86 | 1337 |
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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_d0.012 | | 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_deg1.6 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d23.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.11 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.36 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.24 | 2 | X-RAY DIFFRACTION | c_scbond_it2.06 | 2 | X-RAY DIFFRACTION | c_scangle_it3.05 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.42→2.57 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.313 | 45 | 4.1 % |
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Rwork | 0.236 | 1063 | - |
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obs | - | - | 98.7 % |
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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 | ADP.PARADP.TOPX-RAY DIFFRACTION | 5 | FMN.PARFMN.TOP | | | | | | | | | |
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精密化 | *PLUS 最高解像度: 2.4 Å / 最低解像度: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 |
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溶媒の処理 | *PLUS |
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原子変位パラメータ | *PLUS |
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拘束条件 | *PLUS Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.2 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.11 | | | | |
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