ソフトウェア | 名称 | バージョン | 分類 |
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MOLREP | | 位相決定 | CNS | 1.3 | 精密化 | MOSFLM | | データ削減 | SCALA | | データスケーリング |
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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 1JP5 解像度: 2.4→34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.24 | 1106 | 9.8 % | RANDOM |
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Rwork | 0.2286 | - | - | - |
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obs | 0.2286 | 11290 | 100 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 35.1527 Å2 / ksol: 0.38 e/Å3 |
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原子変位パラメータ | Biso mean: 33.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.898 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.898 Å2 | 0 Å2 |
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3- | - | - | -5.797 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.34 Å | 0.33 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.34 Å | 0.4 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→34 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1836 | 0 | 17 | 133 | 1986 |
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拘束条件 | Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.00922 | 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_deg1.65381 | X-RAY DIFFRACTION | c_angle_deg_na | X-RAY DIFFRACTION | c_angle_deg_prot | X-RAY DIFFRACTION | c_dihedral_angle_d28 | X-RAY DIFFRACTION | c_dihedral_angle_d_na | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | X-RAY DIFFRACTION | c_improper_angle_d0.87 | 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: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.289 | 174 | 9.5 % |
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Rwork | 0.32 | 1664 | - |
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obs | - | - | 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 | DNA-RNA_REP.PARAM | DNA-RNA.TOP | X-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOPX-RAY DIFFRACTION | 5 | CARBOHYDRATE.PARAMCARBOHYDRATE.TOPX-RAY DIFFRACTION | 6 | TRIS.PARAMTRIS.TOPX-RAY DIFFRACTION | 7 | UREA.PARAMUREA.TOPX-RAY DIFFRACTION | 8 | MAM.PARAMMAM.TOP | | | | | | | | | | | | | |
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