ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0419精密化 | XDS | | データ削減 | Aimless | | データスケーリング | MOLREP | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.5→54.755 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.159 / SU B: 1.666 / SU ML: 0.058 / Average fsc free: 0.9627 / Average fsc work: 0.9693 / 交差検証法: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1888 | 2432 | 5.031 % |
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Rwork | 0.1632 | 45904 | - |
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all | 0.164 | - | - |
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obs | - | 48336 | 99.855 % |
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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 BULK SOLVENT |
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原子変位パラメータ | Biso mean: 16.86 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.362 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -1.688 Å2 | 0 Å2 |
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3- | - | - | -0.674 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.5→54.755 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2415 | 0 | 104 | 170 | 2689 |
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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_d0.01 | 0.012 | 2581 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.016 | 2377 | X-RAY DIFFRACTION | r_angle_refined_deg1.863 | 1.824 | 3527 | X-RAY DIFFRACTION | r_angle_other_deg0.671 | 1.765 | 5492 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.881 | 5 | 334 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg6.737 | 5 | 10 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.107 | 10 | 343 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg14.696 | 10 | 103 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 394 | X-RAY DIFFRACTION | r_chiral_restr_other0.04 | 0.2 | 30 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.02 | 3047 | X-RAY DIFFRACTION | r_gen_planes_other0.011 | 0.02 | 563 | X-RAY DIFFRACTION | r_nbd_refined0.24 | 0.2 | 602 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.195 | 0.2 | 2191 | X-RAY DIFFRACTION | r_nbtor_refined0.18 | 0.2 | 1329 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.078 | 0.2 | 1331 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.204 | 0.2 | 139 | X-RAY DIFFRACTION | r_metal_ion_refined0.086 | 0.2 | 5 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.307 | 0.2 | 22 | X-RAY DIFFRACTION | r_nbd_other0.28 | 0.2 | 89 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.221 | 0.2 | 6 | X-RAY DIFFRACTION | r_mcbond_it1.629 | 1.641 | 1327 | X-RAY DIFFRACTION | r_mcbond_other1.628 | 1.641 | 1327 | X-RAY DIFFRACTION | r_mcangle_it2.387 | 2.946 | 1658 | X-RAY DIFFRACTION | r_mcangle_other2.388 | 2.948 | 1659 | X-RAY DIFFRACTION | r_scbond_it2.344 | 1.88 | 1254 | X-RAY DIFFRACTION | r_scbond_other2.341 | 1.88 | 1254 | X-RAY DIFFRACTION | r_scangle_it3.422 | 3.308 | 1867 | X-RAY DIFFRACTION | r_scangle_other3.422 | 3.309 | 1868 | X-RAY DIFFRACTION | r_lrange_it4.429 | 18.676 | 2925 | X-RAY DIFFRACTION | r_lrange_other4.429 | 18.681 | 2926 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Rfactor all | Num. reflection all | Fsc free | Fsc work | % reflection obs (%) | WRfactor Rwork |
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1.5-1.539 | 0.294 | 188 | 0.284 | 3341 | 0.285 | 3538 | 0.922 | 0.915 | 99.7456 | 0.269 | 1.539-1.581 | 0.302 | 179 | 0.266 | 3224 | 0.268 | 3409 | 0.924 | 0.93 | 99.824 | 0.25 | 1.581-1.627 | 0.259 | 169 | 0.24 | 3157 | 0.241 | 3331 | 0.942 | 0.945 | 99.8499 | 0.222 | 1.627-1.677 | 0.25 | 176 | 0.211 | 3085 | 0.213 | 3263 | 0.949 | 0.959 | 99.9387 | 0.194 | 1.677-1.732 | 0.23 | 133 | 0.197 | 3041 | 0.199 | 3178 | 0.961 | 0.967 | 99.8741 | 0.179 | 1.732-1.793 | 0.22 | 145 | 0.184 | 2908 | 0.186 | 3056 | 0.958 | 0.971 | 99.9018 | 0.166 | 1.793-1.86 | 0.226 | 144 | 0.167 | 2783 | 0.169 | 2930 | 0.966 | 0.977 | 99.8976 | 0.151 | 1.86-1.936 | 0.196 | 143 | 0.154 | 2704 | 0.156 | 2851 | 0.975 | 0.983 | 99.8597 | 0.142 | 1.936-2.022 | 0.179 | 147 | 0.148 | 2598 | 0.15 | 2748 | 0.978 | 0.985 | 99.8908 | 0.138 | 2.022-2.121 | 0.172 | 118 | 0.144 | 2486 | 0.146 | 2607 | 0.98 | 0.985 | 99.8849 | 0.137 | 2.121-2.235 | 0.185 | 132 | 0.144 | 2364 | 0.146 | 2500 | 0.974 | 0.986 | 99.84 | 0.139 | 2.235-2.37 | 0.175 | 129 | 0.14 | 2254 | 0.142 | 2386 | 0.981 | 0.987 | 99.8743 | 0.139 | 2.37-2.534 | 0.171 | 103 | 0.138 | 2118 | 0.14 | 2228 | 0.978 | 0.987 | 99.6858 | 0.137 | 2.534-2.736 | 0.172 | 97 | 0.14 | 1987 | 0.141 | 2087 | 0.981 | 0.987 | 99.8563 | 0.14 | 2.736-2.997 | 0.214 | 86 | 0.155 | 1846 | 0.158 | 1936 | 0.968 | 0.985 | 99.7934 | 0.16 | 2.997-3.349 | 0.184 | 83 | 0.157 | 1661 | 0.158 | 1747 | 0.977 | 0.985 | 99.8283 | 0.165 | 3.349-3.865 | 0.139 | 80 | 0.148 | 1483 | 0.147 | 1563 | 0.989 | 0.987 | 100 | 0.159 | 3.865-4.728 | 0.139 | 83 | 0.137 | 1268 | 0.137 | 1351 | 0.987 | 0.989 | 100 | 0.153 | 4.728-6.661 | 0.177 | 65 | 0.173 | 983 | 0.173 | 1052 | 0.982 | 0.986 | 99.6198 | 0.189 | 6.661-54.755 | 0.211 | 32 | 0.17 | 613 | 0.172 | 645 | 0.979 | 0.979 | 100 | 0.182 |
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