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 | | MLPHARE | | 位相決定 | | 直接法 | 5 | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 2 | データ抽出 | | EPICS-based | data aquisition systemデータ収集 | | HKL-3000 | | データ削減 | | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 1.998→62.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.1 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.167 / 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 | 0.237 | 533 | 4.8 % | RANDOM |
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Rwork | 0.219 | - | - | - |
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obs | 0.22 | 11190 | 98.15 % | - |
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all | - | 11190 | - | - |
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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: 44.093 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.53 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.53 Å2 | 0 Å2 |
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3- | - | - | -1.07 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.998→62.62 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1189 | 0 | 0 | 72 | 1261 |
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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_d0.009 | 0.022 | 1215 | X-RAY DIFFRACTION | r_angle_refined_deg1.06 | 1.977 | 1634 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.822 | 5 | 144 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.372 | 24 | 60 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.942 | 15 | 237 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg23.589 | 15 | 9 | X-RAY DIFFRACTION | r_chiral_restr0.095 | 0.2 | 175 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 908 | X-RAY DIFFRACTION | r_nbd_refined0.259 | 0.3 | 591 | X-RAY DIFFRACTION | r_nbtor_refined0.321 | 0.5 | 849 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.192 | 0.5 | 104 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.225 | 0.3 | 23 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.177 | 0.5 | 7 | X-RAY DIFFRACTION | r_mcbond_it3.919 | 1.5 | 740 | X-RAY DIFFRACTION | r_mcangle_it5.006 | 2 | 1175 | X-RAY DIFFRACTION | r_scbond_it7.095 | 3 | 518 | X-RAY DIFFRACTION | r_scangle_it9.833 | 4.5 | 459 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.998→2.05 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.27 | 31 | - |
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Rwork | 0.317 | 695 | - |
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obs | - | 726 | 85.82 % |
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精密化 TLS | 手法: refined / Origin x: 8.3779 Å / Origin y: -22.4167 Å / Origin z: 0.7442 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.0441 Å2 | 0.0299 Å2 | -0.0256 Å2 | - | 0.0604 Å2 | -0.072 Å2 | - | - | -0.033 Å2 |
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L | 1.853 °2 | 0.0847 °2 | 1.1752 °2 | - | 0.5588 °2 | 0.3301 °2 | - | - | 1.714 °2 |
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S | -0.2977 Å ° | -0.0943 Å ° | 0.2868 Å ° | -0.0688 Å ° | 0.1145 Å ° | -0.0708 Å ° | -0.2412 Å ° | -0.2394 Å ° | 0.1832 Å ° |
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