ソフトウェア | 名称 | 分類 |
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CNS | 精密化 | DENZO | データ削減 | SCALEPACK | データスケーリング | CNS | 位相決定 |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.1→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4598334.23 / 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 | 0.275 | 4894 | 8 % | RANDOM |
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Rwork | 0.241 | - | - | - |
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obs | 0.241 | 61181 | 85 % | - |
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all | - | 61181 | - | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 32.6313 Å2 / ksol: 0.299966 e/Å3 |
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原子変位パラメータ | Biso mean: 76.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -16.03 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 33 Å2 | 0 Å2 |
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3- | - | - | -16.96 Å2 |
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Refine analyze | Luzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.77 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6802 | 964 | 0 | 190 | 7956 |
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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_d0.008 | | 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_d21 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.29 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.39 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.38 | 2 | X-RAY DIFFRACTION | c_scbond_it1.93 | 2 | X-RAY DIFFRACTION | c_scangle_it3.03 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.1→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.475 | 640 | 8 % |
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Rwork | 0.482 | 6996 | - |
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obs | - | - | 55.6 % |
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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.TOP | | | | | |
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精密化 | *PLUS 最高解像度: 2.1 Å / 最低解像度: 20 Å / σ(F): 2 / Rfactor obs: 0.241 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.241 |
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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_deg21 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.29 | | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.475 / Rfactor Rwork: 0.482 |
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