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 | | MOLREP | | 位相決定 | | REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | ADSC | Quantumデータ収集 | | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.013→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.6 / SU ML: 0.159 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.216 / 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 | 0.283 | 1210 | 5.1 % | RANDOM |
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Rwork | 0.226 | - | - | - |
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obs | 0.229 | 23633 | 97.68 % | - |
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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: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso max: 56.5 Å2 / Biso mean: 18.772 Å2 / Biso min: 7.89 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.86 Å2 | 0 Å2 | -0.37 Å2 |
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2- | - | 0.06 Å2 | 0 Å2 |
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3- | - | - | -1.23 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.013→30 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2826 | 0 | 16 | 241 | 3083 |
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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_d0.008 | 0.022 | 2936 | X-RAY DIFFRACTION | r_angle_refined_deg1.186 | 1.953 | 3998 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.785 | 5 | 345 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.395 | 22.5 | 148 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.485 | 15 | 442 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.097 | 15 | 28 | X-RAY DIFFRACTION | r_chiral_restr0.083 | 0.2 | 401 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 2330 | X-RAY DIFFRACTION | r_nbd_refined0.192 | 0.2 | 1343 | X-RAY DIFFRACTION | r_nbtor_refined0.308 | 0.2 | 1925 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.144 | 0.2 | 261 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.136 | 0.2 | 41 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.136 | 0.2 | 15 | X-RAY DIFFRACTION | r_mcbond_it0.474 | 1.5 | 1794 | X-RAY DIFFRACTION | r_mcangle_it0.782 | 2 | 2825 | X-RAY DIFFRACTION | r_scbond_it1.183 | 3 | 1331 | X-RAY DIFFRACTION | r_scangle_it1.838 | 4.5 | 1173 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.013→2.065 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.305 | 82 | - |
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Rwork | 0.228 | 1513 | - |
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all | - | 1595 | - |
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obs | - | - | 90.99 % |
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精密化 TLS | 手法: refined / Origin x: 4.5838 Å / Origin y: 0.5889 Å / Origin z: 14.2332 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.0196 Å2 | -0.0001 Å2 | 0.0047 Å2 | - | -0.0219 Å2 | 0.0022 Å2 | - | - | -0.0125 Å2 |
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L | 0.2864 °2 | 0.1482 °2 | -0.1106 °2 | - | 0.2266 °2 | 0.0794 °2 | - | - | 0.4831 °2 |
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S | -0.0225 Å ° | 0.0266 Å ° | 0.0233 Å ° | 0.0071 Å ° | 0.0066 Å ° | 0.0024 Å ° | 0.0176 Å ° | -0.0218 Å ° | 0.0158 Å ° |
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