ソフトウェア | 名称 | バージョン | 分類 | NB |
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d*TREK | | データスケーリング | | CNS | | 精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | CrystalClear | | データ収集 | | d*TREK | | データ削減 | | CNS | | 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 2GIS 解像度: 2.55→19.93 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / 立体化学のターゲット値: Engh & Huber / 詳細: BULK SOLVENT MODEL USED
| Rfactor | 反射数 | %反射 |
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Rfree | 0.293 | 1814 | 9.6 % |
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Rwork | 0.249 | - | - |
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obs | 0.249 | 18805 | 98.9 % |
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all | - | 18976 | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 31.32 Å2 / ksol: 0.35 e/Å3 |
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原子変位パラメータ | Biso mean: 56.66 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 11.52 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 11.52 Å2 | 0 Å2 |
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3- | - | - | -23.04 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.49 Å | 0.41 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.8 Å | 0.71 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.55→19.93 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 2030 | 36 | 48 | 2114 |
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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_deg1.4 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d16.6 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d3.5 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.25 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.54 | 2 | X-RAY DIFFRACTION | c_scbond_it1.43 | 2 | X-RAY DIFFRACTION | c_scangle_it2.21 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.55→2.71 Å / Rfactor Rfree error: 0.025
| Rfactor | 反射数 | %反射 |
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Rfree | 0.426 | 291 | 9.2 % |
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Rwork | 0.408 | 2864 | - |
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obs | - | - | 99.6 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | water_rep.paramdna-rna_rep_revise.top | X-RAY DIFFRACTION | 2 | ion2.paramion2.topX-RAY DIFFRACTION | 3 | dna-rna_rep_revise.param | water.topX-RAY DIFFRACTION | 4 | sam3.paramsam3.top | | | | | |
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