ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | SHELXD | | 位相決定 | RESOLVE | | モデル構築 | ARP | WARPモデル構築 | Coot | | モデル構築 | REFMAC | 5.5.0054精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 位相決定 | RESOLVE | | 位相決定 | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.95→68.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.785 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.21 | 2585 | 5.1 % | RANDOM |
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Rwork | 0.173 | - | - | - |
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all | 0.175 | 50932 | - | - |
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obs | 0.175 | 50932 | 99.66 % | - |
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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: 21.98 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.26 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.31 Å2 | 0 Å2 |
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3- | - | - | -1.57 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→68.52 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4735 | 0 | 24 | 519 | 5278 |
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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_d0.015 | 0.022 | 4980 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.417 | 1.973 | 6762 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.547 | 5 | 642 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.663 | 24.078 | 206 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.321 | 15 | 831 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.526 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.092 | 0.2 | 763 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.021 | 3783 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | 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_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | 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_it0.749 | 1.5 | 3178 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.356 | 2 | 5091 | X-RAY DIFFRACTION | r_scbond_it2.693 | 3 | 1802 | X-RAY DIFFRACTION | r_scangle_it4.308 | 4.5 | 1671 | 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: 1.95→2 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.235 | 181 | - |
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Rwork | 0.226 | 3438 | - |
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obs | - | - | 96.95 % |
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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 | 0.5929 | -0.1434 | -0.1254 | 1.3967 | 0.6863 | 2.0713 | -0.0106 | -0.0017 | -0.0431 | 0.1123 | 0.0554 | 0.0513 | -0.1181 | -0.1434 | -0.0448 | 0.0267 | 0.0238 | 0.0128 | 0.0346 | 0.0183 | 0.0135 | 44.5806 | 13.2686 | 19.1719 | 2 | 0.7719 | -0.3691 | 0.303 | 2.0731 | -0.9753 | 2.7573 | 0.013 | -0.0157 | -0.0218 | 0.1376 | 0.0319 | -0.0032 | 0.1636 | 0.0899 | -0.0449 | 0.0379 | 0.0019 | -0.0117 | 0.0252 | 0.0095 | 0.0275 | 50.8079 | -20.5722 | 19.2768 | 3 | 0.9518 | -0.2916 | 0.0108 | 1.1044 | 0.2633 | 2.2414 | 0.0855 | -0.0186 | 0.0408 | -0.1315 | -0.0213 | 0.0005 | 0.1847 | -0.0099 | -0.0642 | 0.054 | 0.0136 | -0.0245 | 0.0291 | -0.0038 | 0.0434 | 51.9881 | -14.0956 | -13.2653 | 4 | 0.7265 | -0.4003 | -0.1001 | 1.9387 | -0.5222 | 1.6821 | 0.0124 | 0.0028 | -0.0562 | -0.0992 | 0.0359 | -0.0524 | -0.1086 | -0.0433 | -0.0484 | 0.0442 | 0.0357 | -0.0084 | 0.0478 | -0.0267 | 0.0282 | 41.7763 | 18.9204 | -13.0147 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A0 - 153 | 2 | X-RAY DIFFRACTION | 2 | B0 - 153 | 3 | X-RAY DIFFRACTION | 3 | C0 - 154 | 4 | X-RAY DIFFRACTION | 4 | D0 - 152 | | | | |
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