ソフトウェア | 名称 | バージョン | 分類 |
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X-PLOR | | モデル構築 | CNS | 0.1 | 精密化 | X-PLOR | | 精密化 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | X-PLOR | | 位相決定 |
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精密化 | 構造決定の手法: DIFFERENCE FOURIER FROM PREVIOUSLY DETERMINED, RELATED STRUCTURE 開始モデル: UNLIGANDED ECORL 解像度: 1.9→6 Å / Rfactor Rfree error: 0.006 / 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 | 0.2 | 939 | 3.1 % | RANDOM |
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Rwork | 0.18 | - | - | - |
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obs | 0.18 | 30841 | 99.1 % | - |
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原子変位パラメータ | Biso mean: 25.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.95 Å2 | 0 Å2 | 0.49 Å2 |
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2- | - | 1.56 Å2 | 0 Å2 |
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3- | - | - | 1.39 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.19 Å | 0.19 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.08 Å | 0.07 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→6 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1855 | 0 | 97 | 167 | 2119 |
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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_d0.005 | | 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_d27 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.2 | | 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_it2.08 | 2 | X-RAY DIFFRACTION | c_scbond_it2.44 | 2 | X-RAY DIFFRACTION | c_scangle_it3.65 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.9→1.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.224 | 76 | 3 % |
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Rwork | 0.217 | 2497 | - |
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obs | - | - | 85.3 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PARAM19X.PROTOPH19X.PROX-RAY DIFFRACTION | 2 | CARBOHYDRATE.PARAMCARBOHYDRATE.TOPX-RAY DIFFRACTION | 3 | PARHCSDX.PROTOPHCSDX.PRO | | | | | |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.1 / 分類: refinement |
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精密化 | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.18 |
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溶媒の処理 | *PLUS |
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原子変位パラメータ | *PLUS |
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拘束条件 | *PLUS Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg27 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.2 | | | | |
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