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 | MAR345 | | データ収集 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | REFMAC | | 位相決定 | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB ENTRY 1R5D 解像度: 1.53→25.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094 / 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 | 0.23272 | 1785 | 5 % | RANDOM |
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Rwork | 0.2011 | - | - | - |
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obs | 0.20273 | 33874 | 98.11 % | - |
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all | - | 35718 | - | - |
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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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Refine analyze | Luzzati coordinate error obs: 0.228 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.53→25.2 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1882 | 0 | 50 | 313 | 2245 |
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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_d0.007 | 0.022 | 1974 | X-RAY DIFFRACTION | r_angle_refined_deg1.125 | 1.977 | 2666 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.498 | 5 | 246 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.051 | 24.865 | 74 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.233 | 15 | 362 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.376 | 15 | 8 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1420 | X-RAY DIFFRACTION | r_nbd_refined0.185 | 0.2 | 961 | X-RAY DIFFRACTION | r_nbtor_refined0.291 | 0.2 | 1355 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.119 | 0.2 | 231 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.157 | 0.2 | 52 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.119 | 0.2 | 33 | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.53→1.57 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.239 | 121 | - |
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Rwork | 0.213 | 2317 | - |
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obs | - | - | 91.83 % |
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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 | 2.8589 | 0.7204 | -0.8993 | 3.1232 | -1.1689 | 5.9216 | 0.0756 | -0.2529 | 0.0719 | 0.0846 | -0.1427 | -0.0135 | -0.0382 | 0.234 | 0.0672 | 0.031 | -0.0069 | -0.001 | 0.0616 | -0.0097 | 0.0321 | 9.6039 | 20.4649 | 19.1993 | 2 | 4.139 | 1.3146 | -0.5313 | 1.3966 | -0.1664 | 1.2404 | 0.0597 | -0.1845 | 0.0404 | -0.0198 | -0.0558 | 0.0773 | -0.0934 | -0.0179 | -0.0039 | 0.0749 | 0.0195 | -0.018 | 0.0249 | -0.007 | 0.0576 | 28.2259 | 31.0047 | 4.7705 | 3 | 2.315 | 1.0822 | 0.5155 | 2.295 | 0.9056 | 1.2023 | 0.0397 | 0.088 | 0.1076 | -0.1837 | -0.002 | 0.1323 | -0.1683 | 0.0802 | -0.0377 | 0.114 | 0.0152 | -0.0191 | 0.0031 | 0.0268 | 0.0219 | 34.6112 | 39.1262 | 1.2568 | 4 | 2.3387 | 0.4959 | 0.8632 | 1.7754 | 0.0485 | 1.0541 | -0.0786 | -0.1603 | 0.2074 | 0.0144 | -0.0079 | 0.2745 | -0.1289 | -0.1028 | 0.0865 | 0.0732 | 0.0281 | -0.0161 | 0.0226 | -0.0037 | 0.0605 | 29.5 | 36.0976 | 4.9129 | 5 | 3.5523 | 2.0478 | -0.4489 | 1.3168 | -0.1708 | 0.6745 | -0.1198 | -0.1003 | -0.0852 | -0.0048 | 0.0017 | -0.017 | 0.0296 | 0.0088 | 0.1181 | 0.0593 | 0.0189 | 0.012 | 0.0308 | 0.0203 | 0.0616 | 27.2896 | 24.6022 | 7.2108 | 6 | 2.2057 | 0.0884 | -0.1744 | 2.1298 | -1.146 | 2.5048 | -0.0055 | -0.2372 | -0.0556 | -0.0919 | -0.0216 | -0.0394 | 0.1775 | 0.0078 | 0.0271 | 0.0554 | 0.0052 | -0.007 | 0.0641 | -0.0009 | 0.0229 | 6.905 | 15.0867 | 15.9404 | 7 | 1.3274 | 0.7387 | 0.0432 | 2.3634 | -2.0524 | 2.3529 | -0.0492 | -0.0921 | -0.0084 | -0.3124 | 0.1489 | 0.0538 | 0.3586 | -0.2821 | -0.0996 | 0.1055 | -0.0332 | -0.0223 | 0.0339 | -0.0135 | -0.0019 | 2.0666 | 10.1284 | 14.4227 | 8 | 0.8913 | 0.3519 | -0.416 | 1.4759 | -0.9493 | 2.2398 | -0.0529 | -0.03 | -0.0504 | -0.2636 | -0.055 | -0.249 | 0.3931 | 0.1256 | 0.1079 | 0.1079 | 0.0309 | 0.0451 | 0.0161 | -0.0026 | 0.0279 | 10.5491 | 11.7727 | 13.132 |
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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 - 17 | 1 - 17 | 2 | X-RAY DIFFRACTION | 2 | AA18 - 63 | 18 - 63 | 3 | X-RAY DIFFRACTION | 3 | AA64 - 87 | 64 - 87 | 4 | X-RAY DIFFRACTION | 4 | AA88 - 124 | 88 - 124 | 5 | X-RAY DIFFRACTION | 5 | BB1 - 32 | 1 - 32 | 6 | X-RAY DIFFRACTION | 6 | BB33 - 65 | 33 - 65 | 7 | X-RAY DIFFRACTION | 7 | BB66 - 85 | 66 - 85 | 8 | X-RAY DIFFRACTION | 8 | BB86 - 124 | 86 - 124 | | | | | | | | | | | | | | | | |
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