ソフトウェア | 名称 | バージョン | 分類 |
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SCALEPACK | | データスケーリング | MOLREP | | 位相決定 | CNS | 1.1 | 精密化 |
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精密化 | 構造決定の手法: 分子置換 開始モデル: Homology model (Swiss Model)based on PDB Entry 1M1S 解像度: 2→19.56 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 525587.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 1 / 立体化学のターゲット値: Engh & Huber 詳細: In initial stages restrained NCS was used, but later the two monomers were refined independently
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.274 | 560 | 5.2 % | RANDOM |
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Rwork | 0.225 | - | - | - |
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all | 0.238 | 11037 | - | - |
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obs | 0.225 | 11037 | 85.9 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 53.6843 Å2 / ksol: 0.363445 e/Å3 |
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原子変位パラメータ | Biso mean: 26.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -8.1 Å2 | 0 Å2 | -4.09 Å2 |
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2- | - | -8.84 Å2 | 0 Å2 |
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3- | - | - | 16.94 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.31 Å | 0.25 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.26 Å | 0.13 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2→19.56 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1514 | 0 | 0 | 157 | 1671 |
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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_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d28.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.98 | | X-RAY DIFFRACTION | c_mcbond_it1.26 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.73 | 2 | X-RAY DIFFRACTION | c_scbond_it2.12 | 2 | X-RAY DIFFRACTION | c_scangle_it2.81 | 2.5 | | | | | | | | |
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LS精密化 シェル | 解像度: 2→2.13 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.315 | 56 | 4.4 % |
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Rwork | 0.237 | 1214 | - |
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obs | - | 1214 | 65.8 % |
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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 | WATER_REP.PARAMWATER.TOP | | | |
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精密化 | *PLUS 最高解像度: 2.2 Å / 最低解像度: 24.79 Å / Num. reflection obs: 8637 / % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.224 |
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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_bond_d0.007 | X-RAY DIFFRACTION | c_angle_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg28.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.98 | | | | | | |
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LS精密化 シェル | *PLUS 最高解像度: 2.2 Å / 最低解像度: 2.34 Å / Rfactor Rfree: 0.327 / Rfactor Rwork: 0.207 / Num. reflection Rwork: 1217 / Rfactor obs: 0.237 |
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