ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | SHELX | | 位相決定 | | RESOLVE | | 位相決定 | | REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3.004 | データ抽出 | | SHELXD | | 位相決定 | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.76→46.63 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.425 / SU ML: 0.248 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.961 / ESU R Free: 0.348 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.259 | 3502 | 5.1 % | RANDOM |
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Rwork | 0.2 | - | - | - |
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obs | 0.203 | 69168 | 100 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 25.373 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.98 Å2 | 0 Å2 | 2.51 Å2 |
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2- | - | -1.84 Å2 | 0 Å2 |
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3- | - | - | 1.08 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.76→46.63 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 14362 | 0 | 0 | 627 | 14989 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.017 | 0.022 | 14650 | X-RAY DIFFRACTION | r_angle_refined_deg1.892 | 1.953 | 19899 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg10.396 | 5 | 1899 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg40.429 | 24.864 | 623 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg20.497 | 15 | 2365 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.842 | 15 | 70 | X-RAY DIFFRACTION | r_chiral_restr0.129 | 0.2 | 2255 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 11114 | X-RAY DIFFRACTION | r_nbd_refined0.252 | 0.2 | 7137 | X-RAY DIFFRACTION | r_nbtor_refined0.324 | 0.2 | 10068 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.169 | 0.2 | 844 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.189 | 0.2 | 46 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.155 | 0.2 | 4 | X-RAY DIFFRACTION | r_mcbond_it0.868 | 1.5 | 9609 | X-RAY DIFFRACTION | r_mcangle_it1.361 | 2 | 15048 | X-RAY DIFFRACTION | r_scbond_it2.238 | 3 | 5746 | X-RAY DIFFRACTION | r_scangle_it3.619 | 4.5 | 4851 | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION Dom-ID | Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
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1 | A1480 | MEDIUM POSITIONAL0.17 | 0.5 | 2 | B1480 | MEDIUM POSITIONAL0.27 | 0.5 | 3 | C1480 | MEDIUM POSITIONAL0.17 | 0.5 | 4 | D1480 | MEDIUM POSITIONAL0.25 | 0.5 | 1 | A1308 | LOOSE POSITIONAL0.41 | 5 | 2 | B1308 | LOOSE POSITIONAL0.46 | 5 | 3 | C1308 | LOOSE POSITIONAL0.4 | 5 | 4 | D1308 | LOOSE POSITIONAL0.46 | 5 | 1 | A1480 | MEDIUM THERMAL0.75 | 2 | 2 | B1480 | MEDIUM THERMAL1.08 | 2 | 3 | C1480 | MEDIUM THERMAL0.68 | 2 | 4 | D1480 | MEDIUM THERMAL1.02 | 2 | 1 | A1308 | LOOSE THERMAL1.84 | 10 | 2 | B1308 | LOOSE THERMAL2.32 | 10 | 3 | C1308 | LOOSE THERMAL1.9 | 10 | 4 | D1308 | LOOSE THERMAL2.14 | 10 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.76→2.828 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.455 | 214 | - |
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Rwork | 0.3 | 3983 | - |
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all | - | 4197 | - |
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obs | - | - | 100 % |
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