ソフトウェア | 名称 | バージョン | 分類 |
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CNS | 1.1 | 精密化 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | AMoRE | | 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 462D 解像度: 2.4→9.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 605002.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.238 | 519 | 10.4 % | RANDOM |
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Rwork | 0.225 | - | - | - |
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obs | 0.225 | 5001 | 96.4 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 29.8383 Å2 / ksol: 0.287313 e/Å3 |
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原子変位パラメータ | Biso mean: 40.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -8.13 Å2 | 0 Å2 | -0.63 Å2 |
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2- | - | 13.52 Å2 | 0 Å2 |
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3- | - | - | -5.4 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.39 Å | 0.38 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.57 Å | 0.45 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→9.97 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 1048 | 7 | 82 | 1137 |
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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_d0.004 | | 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_deg0.7 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d10 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.23 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it2.17 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it3.15 | 2 | 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: 2.4→2.55 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.464 | 76 | 10.4 % |
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Rwork | 0.395 | 653 | - |
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obs | - | - | 85.4 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 2 | DNA-RNA.PARAM | DNA-RNA.TOP | X-RAY DIFFRACTION | 3 | ION.PARAMION.TOPX-RAY DIFFRACTION | 4 | BRU_REP.PARAM | | | | | |
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