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 | X-PLOR | 3.843 | 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: 分子置換 開始モデル: 2HMQ 解像度: 1.8→72.12 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 39907.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.249 | 6258 | 8 % | RANDOM |
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Rwork | 0.224 | - | - | - |
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all | - | 88489 | - | - |
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obs | - | 78695 | 83 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 42.4492 Å2 / ksol: 0.397062 e/Å3 |
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原子変位パラメータ | Biso mean: 10.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.92 Å2 | 0 Å2 | 2.28 Å2 |
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2- | - | -2.41 Å2 | 0 Å2 |
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3- | - | - | 1.49 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.26 Å | 0.23 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.26 Å | 0.23 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.8→72.12 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7576 | 0 | 32 | 535 | 8143 |
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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_d0.014 | | 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_d19.7 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.25 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.07 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.51 | 2 | X-RAY DIFFRACTION | c_scbond_it1.71 | 2 | X-RAY DIFFRACTION | c_scangle_it2.33 | 2.5 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.339 | 787 | 8 % |
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Rwork | 0.306 | 9001 | - |
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obs | - | 8610 | 62.1 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | FEO.PARFEO.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER_REP.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.PARAM | | | | | | | |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.843 / 分類: refinement |
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精密化 | *PLUS σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.2 |
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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: 10.8 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 | x_bond_d | | X-RAY DIFFRACTION | x_angle_d | | X-RAY DIFFRACTION | x_angle_deg1.3 | | X-RAY DIFFRACTION | x_dihedral_angle_d | | X-RAY DIFFRACTION | x_dihedral_angle_deg19.7 | | X-RAY DIFFRACTION | x_improper_angle_d | | X-RAY DIFFRACTION | x_improper_angle_deg1.25 | | X-RAY DIFFRACTION | x_mcbond_it | 1.5 | X-RAY DIFFRACTION | x_scbond_it | 2 | X-RAY DIFFRACTION | x_mcangle_it | 2 | X-RAY DIFFRACTION | x_scangle_it | 2.5 | | | | | | | | | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.339 / % reflection Rfree: 8 % / Rfactor Rwork: 0.306 |
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