ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | CrystalClear | | データ収集 | d*TREK | | データ削減 | d*TREK | | データスケーリング | 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: 1Z40, 2CGR 解像度: 2.3→27.95 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.046 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.235 / 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 | 0.25565 | 1899 | 5 % | RANDOM |
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Rwork | 0.20914 | - | - | - |
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all | 0.21152 | 36116 | - | - |
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obs | 0.21152 | 36116 | 100 % | - |
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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: 36.36 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.51 Å2 | 0 Å2 | -0.68 Å2 |
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2- | - | 1.29 Å2 | 0 Å2 |
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3- | - | - | 0.78 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.3→27.95 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5378 | 0 | 0 | 220 | 5598 |
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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 | 5522 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.07 | 1.943 | 7539 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.814 | 5 | 697 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg38.37 | 25.126 | 238 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.476 | 15 | 829 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.465 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.069 | 0.2 | 837 | X-RAY DIFFRACTION | r_gen_planes_refined0.003 | 0.02 | 4247 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.176 | 0.2 | 2235 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.299 | 0.2 | 3664 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.131 | 0.2 | 329 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.157 | 0.2 | 31 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.092 | 0.2 | 13 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.358 | 1.5 | 3600 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.636 | 2 | 5672 | X-RAY DIFFRACTION | r_scbond_it0.915 | 3 | 2228 | X-RAY DIFFRACTION | r_scangle_it1.481 | 4.5 | 1867 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.3→2.359 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.322 | 135 | - |
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Rwork | 0.255 | 2594 | - |
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obs | - | - | 100 % |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 3.8147 | -0.0099 | 0.997 | 0.8949 | 0.0002 | 1.4919 | 0.0345 | 0.0801 | -0.2311 | -0.068 | -0.0356 | 0.0278 | 0.0536 | -0.2013 | 0.0011 | -0.1985 | 0.0041 | 0.0381 | -0.3216 | -0.011 | -0.1919 | 13.6529 | -11.2552 | 40.1561 | 2 | 7.4672 | -0.443 | 1.795 | 2.7463 | -1.2231 | 6.2943 | -0.3979 | 1.1588 | 0.602 | -0.1651 | 0.1074 | -0.281 | -0.4991 | -0.193 | 0.2905 | -0.0214 | -0.0159 | -0.0377 | 0.1751 | 0.1142 | -0.1113 | -10.7983 | 6.6021 | 13.0479 | 3 | 10.728 | 4.3203 | 3.518 | 4.0518 | 0.6608 | 7.8402 | 0.0457 | 0.3174 | 0.1513 | -0.7178 | 0.1366 | 0.8038 | 0.1885 | -0.1428 | -0.1823 | 0.3906 | -0.0021 | -0.1991 | 0.6036 | -0.1803 | 0.1742 | -36.6413 | -8.2443 | -10.2787 | 4 | 6.6203 | -0.3308 | 1.447 | 2.4886 | -1.6121 | 4.1916 | -0.2703 | -0.3738 | -0.0641 | 0.193 | 0.4217 | 0.2591 | -0.3648 | -1.1197 | -0.1514 | -0.1086 | 0.1822 | 0.0409 | 0.3201 | 0.0677 | -0.1845 | -24.5483 | -1.5382 | 28.5288 | 5 | 8.6325 | 0.3447 | -0.9471 | 6.1386 | 7.1022 | 22.2825 | 0.1903 | -0.5626 | -1.1025 | 0.0547 | 0.0276 | 0.147 | 1.9239 | -0.1888 | -0.2179 | 0.2933 | -0.0716 | -0.1872 | 0.505 | 0.0848 | 0.349 | -35.5331 | -18.3923 | 2.6248 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA105 - 438 | 3 - 336 | 2 | X-RAY DIFFRACTION | 2 | LB1 - 106 | 1 - 106 | 3 | X-RAY DIFFRACTION | 3 | LB107 - 213 | 107 - 213 | 4 | X-RAY DIFFRACTION | 4 | HC1 - 110 | 1 - 110 | 5 | X-RAY DIFFRACTION | 5 | HC111 - 210 | 111 - 210 | | | | | | | | | | |
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