ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALA | | データスケーリング | | PHASER | | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 2 | データ抽出 | | MOSFLM | | データ削減 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 2Q73 解像度: 2.2→36.27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.157 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.17 / 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 | 0.24 | 1565 | 5.1 % | RANDOM |
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Rwork | 0.218 | - | - | - |
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obs | 0.219 | 29321 | 94.5 % | - |
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all | - | 30886 | - | - |
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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: 39.73 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.81 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.81 Å2 | 0 Å2 |
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3- | - | - | -1.61 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.2→36.27 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2719 | 0 | 4 | 114 | 2837 |
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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_d0.011 | 0.022 | 2769 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.21 | 1.981 | 3728 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.427 | 5 | 333 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.159 | 26.058 | 137 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.661 | 15 | 522 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg6.095 | 15 | 4 | X-RAY DIFFRACTION | r_chiral_restr0.087 | 0.2 | 411 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 2060 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.202 | 0.2 | 1308 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.302 | 0.2 | 1877 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.137 | 0.2 | 135 | 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_refined0.187 | 0.2 | 65 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.219 | 0.2 | 21 | 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_it0.435 | 1.5 | 1669 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.824 | 2 | 2682 | X-RAY DIFFRACTION | r_scbond_it1.444 | 3 | 1120 | X-RAY DIFFRACTION | r_scangle_it2.312 | 4.5 | 1046 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION Ens-ID | Dom-ID | Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
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1 | 1 | A728 | medium positional0.18 | 0.5 | 2 | 1 | C628 | medium positional0.23 | 0.5 | 3 | 1 | A530 | medium positional0.32 | 0.5 | 3 | 2 | B530 | medium positional0.33 | 0.5 | 3 | 3 | C530 | medium positional0.38 | 0.5 | 3 | 4 | D530 | medium positional0.33 | 0.5 | 1 | 1 | A728 | medium thermal0.31 | 2 | 2 | 1 | C628 | medium thermal0.36 | 2 | 3 | 1 | A530 | medium thermal0.41 | 2 | 3 | 2 | B530 | medium thermal0.45 | 2 | 3 | 3 | C530 | medium thermal0.48 | 2 | 3 | 4 | D530 | medium thermal0.44 | 2 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.2→2.26 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.306 | 60 | - |
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Rwork | 0.266 | 1409 | - |
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obs | - | - | 62.51 % |
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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 | 1.6114 | 0.3541 | -1.0089 | 2.1712 | -0.5454 | 9.1811 | -0.109 | 0.0191 | -0.3605 | 0.0518 | 0.0179 | -0.2884 | 1.3646 | 0.3346 | 0.0911 | 0.0263 | 0.0978 | -0.014 | -0.1893 | -0.0444 | -0.0317 | 4.1937 | 31.5301 | 3.838 | 2 | 1.4705 | 0.2978 | -0.4923 | 2.558 | 0.3717 | 8.1853 | -0.0618 | 0.0546 | -0.3977 | -0.0151 | -0.1392 | -0.0654 | 1.3991 | -0.0884 | 0.2009 | 0.0608 | -0.0125 | 0.022 | -0.2413 | -0.0075 | -0.0809 | -2.187 | 31.0922 | -1.3494 | 3 | 2.0983 | -0.4788 | 1.7734 | 2.0711 | 0.1053 | 6.5499 | -0.1797 | 0.0664 | 0.2797 | -0.0905 | 0.0207 | -0.1562 | -0.9812 | 0.3372 | 0.159 | -0.0519 | -0.0555 | 0.0172 | -0.2218 | -0.038 | -0.1064 | 1.7637 | 56.5664 | -1.3512 | 4 | 1.9511 | -0.1031 | 2.1678 | 2.2929 | 0.3433 | 7.6956 | -0.1547 | -0.0911 | 0.2141 | -0.0203 | -0.049 | -0.0806 | -1.0271 | -0.2412 | 0.2037 | -0.061 | 0.0404 | 0.0052 | -0.2138 | -0.0328 | -0.16 | -3.2503 | 56.2234 | 3.844 |
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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 | AA1 - 90 | 1 - 90 | 2 | X-RAY DIFFRACTION | 2 | BB1 - 90 | 1 - 90 | 3 | X-RAY DIFFRACTION | 3 | CC13 - 90 | 13 - 90 | 4 | X-RAY DIFFRACTION | 4 | DD13 - 90 | 13 - 90 | | | | | | | | |
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