ソフトウェア | 名称 | バージョン | 分類 |
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CBASS | | データ収集 | MOLREP | | 位相決定 | REFMAC | 5.2.0019精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3F2Q 解像度: 3.45→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 40.683 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.511 / 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 | 0.21738 | 258 | 4.6 % | RANDOM |
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Rwork | 0.18089 | - | - | - |
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all | 0.18249 | 5449 | - | - |
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obs | 0.18249 | 5385 | 98.83 % | - |
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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: 110.093 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.61 Å2 | -1.31 Å2 | 0 Å2 |
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2- | - | -2.61 Å2 | 0 Å2 |
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3- | - | - | 3.92 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.343 Å |
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精密化ステップ | サイクル: LAST / 解像度: 3.45→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 2353 | 54 | 1 | 2408 |
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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_d0.004 | 0.021 | 2671 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.043 | 3 | 4155 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_2_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_3_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_4_deg | | | X-RAY DIFFRACTION | r_chiral_restr0.047 | 0.2 | 546 | X-RAY DIFFRACTION | r_gen_planes_refined0.003 | 0.02 | 1164 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.16 | 0.2 | 1018 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.277 | 0.2 | 1604 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.137 | 0.2 | 63 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined0.206 | 0.2 | 13 | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.092 | 0.2 | 13 | 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_it | | | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it | | | X-RAY DIFFRACTION | r_scbond_it0.387 | 3 | 2984 | X-RAY DIFFRACTION | r_scangle_it0.654 | 4.5 | 4155 | 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: 3.45→3.537 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.311 | 21 | - |
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Rwork | 0.267 | 359 | - |
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obs | - | 380 | 92.68 % |
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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 | 9.2031 | 0.7382 | 0.8018 | 1.8652 | 0.0353 | 2.0355 | 0.2089 | 0.0077 | -2.0526 | -0.1872 | -0.0837 | 0.5486 | 0.1837 | -0.5945 | -0.1252 | -0.3727 | -0.0408 | 0.0741 | -0.0927 | 0.0019 | 0.2934 | 18.5045 | 30.366 | 15.5021 | 2 | 10.2192 | -1.0334 | -0.887 | 1.8408 | -0.9087 | 5.1677 | 0.1843 | 0.5813 | -0.7361 | -0.2488 | -0.3457 | -0.2194 | -0.1646 | 0.7462 | 0.1614 | -0.4546 | -0.089 | 0.0964 | -0.1044 | -0.1393 | -0.2734 | 44.9419 | 42.4521 | 9.1412 | 3 | 3.2039 | 2.1977 | 0.3607 | 3.364 | -2.3347 | 5.6342 | 0.1177 | -0.4614 | -0.0573 | 0.7761 | 0.1035 | 0.4351 | -0.5093 | -0.614 | -0.2212 | -0.3856 | 0.1027 | 0.1606 | -0.1337 | -0.0881 | -0.3193 | 17.3495 | 47.6858 | 17.4565 | 4 | 11.8563 | 4.8018 | -8.7706 | 5.9221 | -1.9035 | 8.5756 | 0.1826 | -1.9251 | -1.1013 | 1.7363 | -0.4489 | 1.8328 | -1.1436 | 0.2758 | 0.2662 | 0.5777 | -0.058 | 0.0441 | 0.1885 | 0.356 | 0.2175 | 22.1357 | 33.4764 | 35.0469 | 5 | 8.5759 | -2.0587 | 3.0166 | 7.3064 | -0.9942 | 3.2946 | -0.5811 | -0.3266 | 1.1254 | 0.8839 | 0.3549 | 0.1306 | -1.1412 | -0.4555 | 0.2262 | -0.0646 | 0.1187 | 0.184 | -0.3079 | -0.1462 | -0.3505 | 22.4772 | 60.3776 | 14.7573 |
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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 | X1 - 9 | 2 | X-RAY DIFFRACTION | 1 | X85 - 112 | 3 | X-RAY DIFFRACTION | 2 | X10 - 30 | 4 | X-RAY DIFFRACTION | 3 | X31 - 48 | 5 | X-RAY DIFFRACTION | 4 | X49 - 60 | 6 | X-RAY DIFFRACTION | 5 | X61 - 84 | | | | | | |
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