ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | AMoRE | | 位相決定 | CNS | 1.2 | 精密化 | DPS | | データ削減 | |
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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 355D 解像度: 3.02→14.13 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 783377.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.224 | 136 | 9.3 % | RANDOM |
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Rwork | 0.19 | - | - | - |
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obs | 0.19 | 1468 | 99 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: -4.2811 Å2 / ksol: 0.25 e/Å3 |
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原子変位パラメータ | Biso mean: 40.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 15.7 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 13.48 Å2 | 0 Å2 |
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3- | - | - | -29.18 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.33 Å | 0.35 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.41 Å | 0.52 Å |
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精密化ステップ | サイクル: LAST / 解像度: 3.02→14.13 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 490 | 0 | 27 | 517 |
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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_deg0.9 | X-RAY DIFFRACTION | c_angle_deg_na | X-RAY DIFFRACTION | c_angle_deg_prot | X-RAY DIFFRACTION | c_dihedral_angle_d16.4 | 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_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: 3→3.19 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.406 | 22 | 10.2 % |
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Rwork | 0.369 | 193 | - |
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obs | - | - | 89.2 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 2 | water_rep.paramwater.topX-RAY DIFFRACTION | 3 | formylu.paramformylu.topX-RAY DIFFRACTION | 4 | nobase.paramnobase.topX-RAY DIFFRACTION | 5 | noNH.paramnoNH.top | | | | | | | |
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