ソフトウェア | 名称 | バージョン | 分類 |
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DENZO | | データ削減 | SCALEPACK | | データスケーリング | SHARP | | 位相決定 | CNS | 0.5 | 精密化 |
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精密化 | 解像度: 2→500 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2553955.22 / 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 | 0.21 | 13919 | 10 % | RANDOM |
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Rwork | 0.185 | - | - | - |
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all | - | 139206 | - | - |
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obs | - | 139206 | 88.1 % | - |
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 57.6 Å2 / ksol: 0.388 e/Å3 |
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原子変位パラメータ | Biso mean: 24.5 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.91 Å2 | 0 Å2 | -0.77 Å2 |
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2- | - | -3.71 Å2 | 0 Å2 |
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3- | - | - | -2.2 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.24 Å | 0.2 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.18 Å | 0.14 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2→500 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 15291 | 0 | 472 | 1869 | 17632 |
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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_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.3 | | X-RAY DIFFRACTION | c_improper_angle_d4.04 | | X-RAY DIFFRACTION | c_mcbond_it0.97 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.47 | 2 | X-RAY DIFFRACTION | c_scbond_it1.59 | 2 | X-RAY DIFFRACTION | c_scangle_it2.44 | 2.5 | | | | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Refine-ID | Weight Biso | Weight position |
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1 | 1 | X-RAY DIFFRACTION | 2 | 15 | 2 | 2 | X-RAY DIFFRACTION | 2 | 150 |
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LS精密化 シェル | 解像度: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.248 | 2018 | 10 % |
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Rwork | 0.214 | 18086 | - |
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obs | - | - | 76.8 % |
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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.TOPX-RAY DIFFRACTION | 3 | CIT.PARAMCIT.TOPX-RAY DIFFRACTION | 4 | CARBOHYDRATE.PARAMCARBOHYDRATE.TOPX-RAY DIFFRACTION | 5 | FAD_COV.PARAMFAD_COV.TOP | | | | | | | | | |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.5 / 分類: refinement |
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精密化 | *PLUS 最低解像度: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.21 |
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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: 24.5 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 | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg24.3 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg4.04 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.248 / % reflection Rfree: 10 % / Rfactor Rwork: 0.214 |
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