ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0352精密化 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: Alphafold 解像度: 1.965→78.271 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.291 / SU ML: 0.117 / 交差検証法: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.155 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2262 | 1557 | 4.808 % |
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Rwork | 0.1748 | 30824 | - |
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all | 0.177 | - | - |
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obs | - | 32381 | 99.164 % |
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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: 32.633 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.961 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -1.926 Å2 | 0 Å2 |
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3- | - | - | -1.035 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.965→78.271 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3408 | 0 | 0 | 183 | 3591 |
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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 | 0.011 | 3530 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.016 | 2987 | X-RAY DIFFRACTION | r_angle_refined_deg2.111 | 1.642 | 4819 | X-RAY DIFFRACTION | r_angle_other_deg0.735 | 1.562 | 6980 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.049 | 5 | 432 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg10.55 | 5 | 18 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.102 | 10 | 524 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg16.539 | 10 | 182 | X-RAY DIFFRACTION | r_chiral_restr0.109 | 0.2 | 501 | X-RAY DIFFRACTION | r_gen_planes_refined0.014 | 0.02 | 4107 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 741 | X-RAY DIFFRACTION | r_nbd_refined0.233 | 0.2 | 717 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.201 | 0.2 | 2877 | X-RAY DIFFRACTION | r_nbtor_refined0.189 | 0.2 | 1716 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.09 | 0.2 | 1732 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.16 | 0.2 | 165 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.241 | 0.2 | 20 | X-RAY DIFFRACTION | r_nbd_other0.316 | 0.2 | 70 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.078 | 0.2 | 8 | X-RAY DIFFRACTION | r_mcbond_it4.133 | 3.323 | 1731 | X-RAY DIFFRACTION | r_mcbond_other4.136 | 3.324 | 1731 | X-RAY DIFFRACTION | r_mcangle_it5.348 | 4.94 | 2162 | X-RAY DIFFRACTION | r_mcangle_other5.354 | 4.942 | 2163 | X-RAY DIFFRACTION | r_scbond_it6.438 | 3.669 | 1799 | X-RAY DIFFRACTION | r_scbond_other6.437 | 3.672 | 1800 | X-RAY DIFFRACTION | r_scangle_it8.082 | 5.325 | 2657 | X-RAY DIFFRACTION | r_scangle_other8.081 | 5.327 | 2658 | X-RAY DIFFRACTION | r_lrange_it9.322 | 44.235 | 4083 | X-RAY DIFFRACTION | r_lrange_other9.337 | 43.863 | 4059 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.965-2.016 | 0.304 | 115 | 0.258 | 2245 | 0.261 | 2364 | 0.923 | 0.942 | 99.8308 | 0.244 | 2.016-2.071 | 0.29 | 116 | 0.23 | 2202 | 0.233 | 2321 | 0.938 | 0.958 | 99.8708 | 0.218 | 2.071-2.131 | 0.297 | 113 | 0.214 | 2149 | 0.218 | 2266 | 0.941 | 0.965 | 99.8235 | 0.2 | 2.131-2.196 | 0.249 | 103 | 0.197 | 2051 | 0.199 | 2164 | 0.951 | 0.974 | 99.5379 | 0.183 | 2.196-2.268 | 0.223 | 93 | 0.187 | 2013 | 0.188 | 2108 | 0.966 | 0.977 | 99.9051 | 0.173 | 2.268-2.348 | 0.253 | 110 | 0.181 | 1957 | 0.185 | 2071 | 0.964 | 0.979 | 99.8069 | 0.165 | 2.348-2.436 | 0.229 | 123 | 0.175 | 1896 | 0.178 | 2025 | 0.966 | 0.981 | 99.7037 | 0.162 | 2.436-2.536 | 0.255 | 84 | 0.176 | 1800 | 0.18 | 1888 | 0.963 | 0.981 | 99.7881 | 0.163 | 2.536-2.648 | 0.242 | 81 | 0.183 | 1758 | 0.185 | 1845 | 0.966 | 0.98 | 99.6748 | 0.171 | 2.648-2.778 | 0.294 | 85 | 0.188 | 1669 | 0.193 | 1759 | 0.945 | 0.978 | 99.7157 | 0.179 | 2.778-2.928 | 0.257 | 87 | 0.195 | 1589 | 0.198 | 1689 | 0.961 | 0.976 | 99.2303 | 0.189 | 2.928-3.105 | 0.284 | 77 | 0.191 | 1509 | 0.195 | 1593 | 0.956 | 0.977 | 99.5606 | 0.189 | 3.105-3.319 | 0.205 | 60 | 0.178 | 1443 | 0.179 | 1511 | 0.974 | 0.981 | 99.4706 | 0.184 | 3.319-3.584 | 0.196 | 56 | 0.171 | 1339 | 0.172 | 1403 | 0.977 | 0.984 | 99.4298 | 0.181 | 3.584-3.926 | 0.158 | 59 | 0.155 | 1213 | 0.155 | 1307 | 0.983 | 0.987 | 97.3221 | 0.172 | 3.926-4.388 | 0.171 | 62 | 0.134 | 1083 | 0.136 | 1185 | 0.983 | 0.989 | 96.6245 | 0.157 | 4.388-5.064 | 0.19 | 42 | 0.137 | 998 | 0.139 | 1076 | 0.982 | 0.989 | 96.6543 | 0.162 | 5.064-6.195 | 0.223 | 53 | 0.145 | 832 | 0.15 | 907 | 0.976 | 0.987 | 97.5744 | 0.173 | 6.195-8.734 | 0.157 | 18 | 0.169 | 684 | 0.169 | 728 | 0.982 | 0.982 | 96.4286 | 0.205 | 8.734-78.271 | 0.225 | 20 | 0.196 | 394 | 0.197 | 444 | 0.985 | 0.971 | 93.2432 | 0.275 |
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