ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | SHELXS | | 位相決定 | CNS | 1.3 | 精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.3→47.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 63733.32 / 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 / 詳細: BULK SOLVENT MODEL USED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.25 | 2223 | 9.9 % | RANDOM |
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Rwork | 0.227 | - | - | - |
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obs | 0.227 | 22391 | 95.6 % | - |
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all | - | 23435 | - | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 25.3993 Å2 / ksol: 0.32 e/Å3 |
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原子変位パラメータ | Biso mean: 44 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.4 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -8.75 Å2 | 0 Å2 |
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3- | - | - | 8.34 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.35 Å | 0.33 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.57 Å | 0.58 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.3→47.08 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3852 | 0 | 8 | 71 | 3931 |
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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_d0.007 | | 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_d22.7 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d0.84 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.27 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.17 | 2 | X-RAY DIFFRACTION | c_scbond_it1.88 | 2 | X-RAY DIFFRACTION | c_scangle_it2.84 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.384 | 339 | 10.2 % |
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Rwork | 0.391 | 2979 | - |
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obs | - | - | 86.3 % |
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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.top | | | | | | | |
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