ソフトウェア | 名称 | バージョン | 分類 | NB |
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REFMAC | 5.2.0005精密化 | | XSCALE | | データスケーリング | | PDB_EXTRACT | 1.601 | データ抽出 | | XDS | | データ削減 | | MOLREP | | 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: 1n3bA 解像度: 1.7→28.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.818 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.211 | 1637 | 5.1 % | RANDOM |
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Rwork | 0.178 | - | - | - |
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all | 0.18 | - | - | - |
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obs | 0.17984 | 30645 | 99.77 % | - |
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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 mean: 30.659 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.48 Å2 | 0 Å2 | -1.15 Å2 |
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2- | - | 1.39 Å2 | 0 Å2 |
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3- | - | - | -1.7 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→28.03 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1767 | 0 | 61 | 199 | 2027 |
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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 | 1883 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 1755 | X-RAY DIFFRACTION | r_angle_refined_deg1.724 | 2.001 | 2566 | X-RAY DIFFRACTION | r_angle_other_deg0.858 | 3 | 4079 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.757 | 5 | 234 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.493 | 24.459 | 74 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.581 | 15 | 326 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg13.847 | 15 | 11 | X-RAY DIFFRACTION | r_chiral_restr0.12 | 0.2 | 295 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 2035 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 344 | X-RAY DIFFRACTION | r_nbd_refined0.212 | 0.2 | 359 | X-RAY DIFFRACTION | r_nbd_other0.175 | 0.2 | 1735 | X-RAY DIFFRACTION | r_nbtor_refined0.175 | 0.2 | 913 | X-RAY DIFFRACTION | r_nbtor_other0.086 | 0.2 | 1107 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.18 | 0.2 | 143 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.236 | 0.2 | 6 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.174 | 0.2 | 34 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.267 | 0.2 | 14 | X-RAY DIFFRACTION | r_mcbond_it2.685 | 3 | 1250 | X-RAY DIFFRACTION | r_mcbond_other0.654 | 3 | 473 | X-RAY DIFFRACTION | r_mcangle_it3.466 | 5 | 1854 | X-RAY DIFFRACTION | r_scbond_it5.497 | 8 | 812 | X-RAY DIFFRACTION | r_scangle_it7.518 | 11 | 709 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.7→1.744 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.336 | 121 | - |
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Rwork | 0.27 | 2216 | - |
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obs | - | - | 99.74 % |
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精密化 TLS | 手法: refined / Origin x: -0.3825 Å / Origin y: 30.5271 Å / Origin z: 25.6603 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.048 Å2 | 0.0143 Å2 | -0.0224 Å2 | - | -0.1022 Å2 | -0.0185 Å2 | - | - | -0.0398 Å2 |
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L | 0.7757 °2 | 0.092 °2 | -0.1657 °2 | - | 0.8049 °2 | -0.7231 °2 | - | - | 3.5913 °2 |
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S | -0.0138 Å ° | -0.0993 Å ° | 0.0068 Å ° | -0.2816 Å ° | -0.008 Å ° | 0.1382 Å ° | 0.0841 Å ° | 0.2368 Å ° | 0.0218 Å ° |
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