ソフトウェア | 名称 | バージョン | 分類 |
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X-PLOR | 3.1 | モデル構築 | X-PLOR | 3.1 | 精密化 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | X-PLOR | 3.1 | 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 2PAZ 解像度: 2.5→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / 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 | 0.239 | 402 | 4 % | RANDOM |
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Rwork | 0.189 | - | - | - |
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obs | 0.189 | 10531 | 86 % | - |
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原子変位パラメータ | Biso mean: 26.3 Å2 |
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Refine analyze | Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.4 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.5→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1926 | 0 | 2 | 56 | 1984 |
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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 | x_bond_d0.01 | | X-RAY DIFFRACTION | x_bond_d_na | | X-RAY DIFFRACTION | x_bond_d_prot | | X-RAY DIFFRACTION | x_angle_d | | X-RAY DIFFRACTION | x_angle_d_na | | X-RAY DIFFRACTION | x_angle_d_prot | | X-RAY DIFFRACTION | x_angle_deg1.6 | | X-RAY DIFFRACTION | x_angle_deg_na | | X-RAY DIFFRACTION | x_angle_deg_prot | | X-RAY DIFFRACTION | x_dihedral_angle_d27 | | X-RAY DIFFRACTION | x_dihedral_angle_d_na | | X-RAY DIFFRACTION | x_dihedral_angle_d_prot | | X-RAY DIFFRACTION | x_improper_angle_d1.38 | | X-RAY DIFFRACTION | x_improper_angle_d_na | | X-RAY DIFFRACTION | x_improper_angle_d_prot | | X-RAY DIFFRACTION | x_mcbond_it | 1.5 | X-RAY DIFFRACTION | x_mcangle_it | 2 | X-RAY DIFFRACTION | x_scbond_it | 2 | X-RAY DIFFRACTION | x_scangle_it | 2.5 | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | NCS model details: RESTRAINED |
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LS精密化 シェル | 解像度: 2.5→2.6 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
| Rfactor | 反射数 | %反射 |
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Rfree | 0.36 | 40 | 2.7 % |
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Rwork | 0.28 | 979 | - |
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obs | - | - | 67.44 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PARCHCSDX.PROTOPH19.PEPX-RAY DIFFRACTION | 2 | PARAM11.WAT | | | |
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精密化 | *PLUS 最低解像度: 20 Å / Num. reflection obs: 10129 / Rfactor obs: 0.189 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.189 |
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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 | x_bond_d0.01 | X-RAY DIFFRACTION | x_dihedral_angle_d | X-RAY DIFFRACTION | x_dihedral_angle_deg26.6 | X-RAY DIFFRACTION | x_improper_angle_d | X-RAY DIFFRACTION | x_improper_angle_deg1.38 | | | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.36 / Rfactor Rwork: 0.28 |
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