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 | 0.4 | 精密化 | DENZO | | データ削減 | SCALEPACK | | データスケーリング |
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精密化 | 解像度: 2.8→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 578374.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.289 | 640 | 8.3 % | RANDOM |
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Rwork | 0.222 | - | - | - |
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obs | 0.222 | 7679 | 98.1 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 85.64 Å2 / ksol: 0.42 e/Å3 |
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原子変位パラメータ | Biso mean: 61.5 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -5.97 Å2 | 2.6 Å2 | 0 Å2 |
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2- | - | -5.97 Å2 | 0 Å2 |
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3- | - | - | 11.95 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.5 Å | 0.36 Å |
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Luzzati d res low | - | 8 Å |
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Luzzati sigma a | 0.37 Å | 0.28 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.8→8 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 721 | 1221 | 12 | 27 | 1981 |
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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_d0.006 | | 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_d16.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.97 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it4.34 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it6.73 | 2 | X-RAY DIFFRACTION | c_scbond_it6.69 | 2 | X-RAY DIFFRACTION | c_scangle_it9.17 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.8→2.97 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.442 | 101 | 8.6 % |
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Rwork | 0.346 | 1078 | - |
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obs | - | - | 92.3 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | LUC.PARAMDNA-RNA.TOP | X-RAY DIFFRACTION | 2 | WATER_REP.PARAWATER.TOPX-RAY DIFFRACTION | 3 | ION2.PARAMION.TOPX-RAY DIFFRACTION | 4 | PROTEIN_REP.PA | | | | | | |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.4 / 分類: refinement |
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精密化 | *PLUS σ(F): 2 / % reflection Rfree: 8.3 % |
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溶媒の処理 | *PLUS |
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原子変位パラメータ | *PLUS Biso mean: 61.5 Å2 |
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拘束条件 | *PLUS Refine-ID | タイプ | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg16.4 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg1.97 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.442 / % reflection Rfree: 8.6 % / Rfactor Rwork: 0.346 |
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