ソフトウェア | 名称 | バージョン | 分類 | NB |
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d*TREK | | データスケーリング | | d*TREK | 9.7Dデータ削減 | | REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | CrystalClear | | データ収集 | | PHASER | | 位相決定 | | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3LF6 解像度: 1.95→30.31 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.918 / SU ML: 0.115 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / 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 | 0.2492 | 1249 | 5.1 % | RANDOM |
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Rwork | 0.204 | - | - | - |
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obs | 0.2063 | 23184 | 99.66 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso max: 70.68 Å2 / Biso mean: 44.3047 Å2 / Biso min: 26.73 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.02 Å2 | 0 Å2 | -0.02 Å2 |
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2- | - | 0.01 Å2 | 0 Å2 |
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3- | - | - | -0.03 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→30.31 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2394 | 0 | 0 | 194 | 2588 |
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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 | 2496 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 1615 | X-RAY DIFFRACTION | r_angle_refined_deg1.04 | 1.945 | 3423 | X-RAY DIFFRACTION | r_angle_other_deg0.775 | 3 | 3963 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.711 | 5 | 321 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg31.994 | 24.286 | 112 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.06 | 15 | 391 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.399 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.062 | 0.2 | 397 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 2800 | X-RAY DIFFRACTION | r_gen_planes_other0 | 0.02 | 489 | X-RAY DIFFRACTION | r_nbd_refined0.204 | 0.3 | 509 | X-RAY DIFFRACTION | r_nbd_other0.201 | 0.3 | 1784 | X-RAY DIFFRACTION | r_nbtor_refined0.181 | 0.5 | 1232 | X-RAY DIFFRACTION | r_nbtor_other0.088 | 0.5 | 1217 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.19 | 0.5 | 261 | X-RAY DIFFRACTION | r_xyhbond_nbd_other0.006 | 0.5 | 1 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.087 | 0.3 | 7 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.377 | 0.3 | 27 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.207 | 0.5 | 19 | X-RAY DIFFRACTION | r_mcbond_it0.936 | 2 | 1605 | X-RAY DIFFRACTION | r_mcbond_other0.196 | 2 | 621 | X-RAY DIFFRACTION | r_mcangle_it1.535 | 3 | 2566 | X-RAY DIFFRACTION | r_scbond_it1.987 | 4 | 1001 | X-RAY DIFFRACTION | r_scangle_it2.94 | 6 | 849 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.95→2.001 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.29 | 95 | - |
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Rwork | 0.244 | 1720 | - |
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all | - | 1815 | - |
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obs | - | - | 99.51 % |
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