ソフトウェア | 名称 | バージョン | 分類 |
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SCALEPACK | | データスケーリング | REFMAC | 5.8.0103精密化 | PDB_EXTRACT | 3.2 | データ抽出 | DENZO | | データ削減 | MOLREP | | モデル構築 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4MB6 解像度: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.718 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1433 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2121 | 834 | 5.1 % | RANDOM |
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Rwork | 0.1867 | - | - | - |
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obs | 0.1881 | 15497 | 91.25 % | - |
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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 |
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原子変位パラメータ | Biso max: 66.43 Å2 / Biso mean: 26.827 Å2 / Biso min: 12.53 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.21 Å2 | 0 Å2 | 0.26 Å2 |
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2- | - | -1.62 Å2 | 0 Å2 |
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3- | - | - | 1.71 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.9→48.2 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1355 | 0 | 26 | 37 | 1418 |
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Biso mean | - | - | 20.97 | 28.76 | - |
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残基数 | - | - | - | - | 179 |
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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_d0.023 | 0.019 | 1433 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 1382 | X-RAY DIFFRACTION | r_angle_refined_deg2.306 | 2.007 | 1956 | X-RAY DIFFRACTION | r_angle_other_deg0.915 | 3 | 3195 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.586 | 5 | 186 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.09 | 24.259 | 54 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.922 | 15 | 238 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.748 | 15 | 7 | X-RAY DIFFRACTION | r_chiral_restr0.137 | 0.2 | 232 | X-RAY DIFFRACTION | r_gen_planes_refined0.012 | 0.021 | 1599 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 299 | X-RAY DIFFRACTION | r_mcbond_it1.073 | 0.996 | 729 | X-RAY DIFFRACTION | r_mcbond_other1.071 | 0.992 | 728 | X-RAY DIFFRACTION | r_mcangle_it1.852 | 1.48 | 914 | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.901→1.95 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.318 | 47 | - |
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Rwork | 0.213 | 759 | - |
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all | - | 806 | - |
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obs | - | - | 60.97 % |
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精密化 TLS | 手法: refined / Origin x: 21.7073 Å / Origin y: -0.734 Å / Origin z: 7.1657 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2455 Å2 | -0.0443 Å2 | 0.0313 Å2 | - | 0.181 Å2 | -0.0168 Å2 | - | - | 0.0441 Å2 |
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L | 1.0448 °2 | -0.146 °2 | -0.5316 °2 | - | 0.4966 °2 | -0.2788 °2 | - | - | 1.2629 °2 |
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S | 0.3103 Å ° | -0.0624 Å ° | 0.0333 Å ° | 0.1131 Å ° | -0.1209 Å ° | 0.1241 Å ° | -0.119 Å ° | -0.1097 Å ° | -0.1895 Å ° |
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