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 | HKL-2000 | | データ収集 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | SOLVE | | 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: 2.87→113.23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.875 / SU B: 45.038 / SU ML: 0.403 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R Free: 0.514 / 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 | 0.31844 | 1030 | 9.9 % | RANDOM |
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Rwork | 0.24986 | - | - | - |
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obs | 0.2566 | 9414 | 96.32 % | - |
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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: 75.861 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.04 Å2 | 0 Å2 | 3.66 Å2 |
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2- | - | -3.24 Å2 | 0 Å2 |
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3- | - | - | 6.58 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.87→113.23 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2704 | 0 | 0 | 0 | 2704 |
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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_d0.013 | 0.022 | 2733 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.496 | 1.981 | 3688 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.755 | 5 | 342 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg42.646 | 25.821 | 134 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg21.527 | 15 | 531 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg28.308 | 15 | 19 | X-RAY DIFFRACTION | r_chiral_restr0.095 | 0.2 | 433 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 2024 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.253 | 0.2 | 1404 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.312 | 0.2 | 1876 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.17 | 0.2 | 127 | 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_refined0.245 | 0.2 | 27 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.272 | 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_it0.497 | 1.5 | 1761 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.843 | 2 | 2767 | X-RAY DIFFRACTION | r_scbond_it1.461 | 3 | 1070 | X-RAY DIFFRACTION | r_scangle_it2.321 | 4.5 | 921 | 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: 2.871→2.945 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.499 | 61 | - |
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Rwork | 0.303 | 542 | - |
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obs | - | - | 76.33 % |
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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 | 7.8579 | -0.5155 | -5.5245 | 1.1601 | 0.8631 | 5.7807 | -0.9162 | -1.3701 | -1.3809 | 0.7769 | 0.1546 | 0.374 | 1.2536 | 0.3077 | 0.7617 | 0.0759 | 0.033 | 0.1831 | 0.0492 | 0.3454 | 0.3162 | 4.2524 | 23.9304 | 28.7648 | 2 | 2.8655 | 0.1918 | -0.6715 | 7.6006 | -6.8455 | 9.5998 | -0.0663 | -1.1019 | -0.0486 | 1.5766 | 0.4751 | 0.7648 | -0.8219 | -0.6885 | -0.4088 | -0.1534 | 0.0969 | 0.072 | -0.0419 | -0.0425 | -0.3843 | -5.1056 | 49.6215 | 24.2753 |
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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 | AA360 - 410 | 6 - 56 | 2 | X-RAY DIFFRACTION | 1 | AA540 - 642 | 186 - 288 | 3 | X-RAY DIFFRACTION | 2 | AA411 - 539 | 57 - 185 | 4 | X-RAY DIFFRACTION | 2 | AA643 - 702 | 289 - 348 | | | | | | | | |
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