ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | MOLREP | | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | CrystalClear | | データ収集 | | HKL-2000 | | データ削減 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.368 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2813 / 交差検証法: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.21 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: U VALUES : RESIDUAL ONLY
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.23405 | 1406 | 5 % | RANDOM |
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Rwork | 0.18336 | - | - | - |
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obs | 0.18586 | 26615 | 90.34 % | - |
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all | - | 31017 | - | - |
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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: 41.195 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.03 Å2 | 0 Å2 | -2.34 Å2 |
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2- | - | -0.88 Å2 | 0 Å2 |
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3- | - | - | -0.6 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4172 | 0 | 82 | 127 | 4381 |
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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_d0.014 | 0.022 | 4357 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.661 | 1.952 | 5867 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.527 | 5 | 502 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.554 | 25.225 | 222 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.788 | 15 | 782 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.545 | 15 | 10 | X-RAY DIFFRACTION | r_chiral_restr0.123 | 0.2 | 590 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 3316 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.678 | 1.5 | 2502 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.272 | 2 | 4022 | X-RAY DIFFRACTION | r_scbond_it2.242 | 3 | 1855 | X-RAY DIFFRACTION | r_scangle_it3.609 | 4.5 | 1845 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.098→2.152 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.241 | 71 | - |
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Rwork | 0.21 | 1292 | - |
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obs | - | - | 60.1 % |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 2.8303 | -0.5151 | 0.6794 | 1.8994 | 0.125 | 1.9966 | -0.0192 | -0.0788 | 0.032 | 0.1069 | -0.0016 | 0.0334 | 0.0063 | -0.0166 | 0.0207 | 0.0077 | -0.0038 | 0.0026 | 0.0092 | -0.0024 | 0.0015 | -6.275 | -0.662 | 23.169 | 2 | 1.501 | 0.2249 | 0.0352 | 2.4297 | -0.6115 | 3.0413 | -0.0185 | 0.0897 | -0.0952 | -0.0732 | -0.0402 | 0.0055 | 0.1119 | 0.054 | 0.0587 | 0.0592 | 0.004 | -0.0366 | 0.0256 | 0.0084 | 0.0596 | -17.591 | -25.297 | -1.028 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A2 - 254 | 2 | X-RAY DIFFRACTION | 2 | B2 - 254 | | |
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