ソフトウェア | 名称 | バージョン | 分類 |
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SHARP | | 位相決定 | CNS | 1.2 | 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: 2.9→47.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 60190.76 / 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: 1. SF file contains Friedel pairs 2. BULK SOLVENT MODEL USED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.286 | 1844 | 5 % | RANDOM |
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Rwork | 0.24 | - | - | - |
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obs | 0.24 | 36616 | 99.5 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 43.3582 Å2 / ksol: 0.35 e/Å3 |
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原子変位パラメータ | Biso mean: 71.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 9.19 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 9.19 Å2 | 0 Å2 |
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3- | - | - | -18.39 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.48 Å | 0.39 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 1.02 Å | 0.71 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.9→47.48 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3348 | 1665 | 31 | 0 | 5044 |
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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_d1.54 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.35 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.38 | 2 | X-RAY DIFFRACTION | c_scbond_it2.1 | 2 | X-RAY DIFFRACTION | c_scangle_it3.47 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.427 | 321 | 5.5 % |
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Rwork | 0.37 | 5555 | - |
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obs | - | - | 95.2 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | protein_rep.paramCprotein.topX-RAY DIFFRACTION | 2 | dna-rna_rep.param | Cdna-rna.top | X-RAY DIFFRACTION | 3 | atp_par_2.txtatp.topX-RAY DIFFRACTION | 4 | TPO-100907.param | TPO-100907.top | | | | |
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