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 | SBC-Collect | | データ収集 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | SHELXD | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | 位相決定 | RESOLVE | | 位相決定 | HKL-3000 | | 位相決定 | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.75→48.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.374 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.323 / ESU R Free: 0.379 / 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 | 0.27272 | 1178 | 5.1 % | RANDOM |
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Rwork | 0.20679 | - | - | - |
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all | 0.21007 | 21778 | - | - |
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obs | 0.21007 | 21778 | 99.14 % | - |
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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: 51.545 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.13 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.13 Å2 | 0 Å2 |
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3- | - | - | 0.27 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.75→48.56 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5304 | 0 | 22 | 30 | 5356 |
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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_d0.018 | 0.022 | 5405 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.926 | 1.99 | 7294 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.068 | 5 | 664 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg41.166 | 26.09 | 266 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg24.867 | 15 | 1016 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg23.114 | 15 | 24 | X-RAY DIFFRACTION | r_chiral_restr0.144 | 0.2 | 846 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 4016 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.275 | 0.2 | 2748 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.337 | 0.2 | 3753 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.169 | 0.2 | 196 | 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_refined0.275 | 0.2 | 75 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.122 | 0.2 | 4 | 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_it1.123 | 2 | 3385 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.853 | 3 | 5394 | X-RAY DIFFRACTION | r_scbond_it1.104 | 2 | 2165 | X-RAY DIFFRACTION | r_scangle_it1.725 | 3 | 1899 | 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: 2.75→2.82 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.403 | 94 | - |
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Rwork | 0.329 | 1443 | - |
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obs | - | 1537 | 90.79 % |
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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 | 7.2462 | -4.6518 | 0.9057 | 6.8477 | -2.2633 | 3.4215 | -0.2526 | -0.7485 | -0.1959 | 1.092 | 0.3597 | 0.2174 | -0.188 | -0.2384 | -0.107 | 0.1589 | 0.0279 | 0.1122 | -0.2225 | 0.0565 | -0.3201 | 32.024 | -6.534 | 158.149 | 2 | 5.4253 | -4.3523 | 1.6657 | 5.1197 | -2.4123 | 2.435 | -0.1728 | -0.2846 | -0.2563 | 0.3336 | -0.0075 | 0.3087 | -0.2003 | -0.1369 | 0.1803 | -0.1383 | 0.0578 | 0.0816 | -0.133 | -0.0417 | -0.0794 | 4.659 | 24.485 | 137.896 | 3 | 6.9168 | -4.1601 | -1.344 | 7.2818 | 0.56 | 3.526 | 0.443 | 0.6181 | 0.7561 | -1.0334 | -0.4246 | -0.0299 | -0.5817 | -0.3349 | -0.0184 | -0.0229 | 0.1247 | -0.0277 | -0.0282 | 0.1285 | -0.2187 | 25.665 | 26.766 | 117.768 | 4 | 2.4675 | -2.2799 | 0.2886 | 7.3335 | -2.1177 | 2.6545 | -0.0517 | -0.0221 | -0.1628 | -0.0566 | -0.1025 | -0.6447 | 0.1116 | 0.2725 | 0.1542 | -0.2712 | 0.0283 | 0.0123 | -0.1674 | 0.0229 | -0.2967 | 44.548 | -11.39 | 132.855 |
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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 | AA6 - 172 | 9 - 175 | 2 | X-RAY DIFFRACTION | 2 | BB4 - 172 | 7 - 175 | 3 | X-RAY DIFFRACTION | 3 | CC6 - 172 | 9 - 175 | 4 | X-RAY DIFFRACTION | 4 | DD5 - 172 | 8 - 175 | | | | | | | | |
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