ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0415精密化 | XDS | | データ削減 | MOLREP | | 位相決定 | ARP/wARP | | モデル構築 | Aimless | | 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 / 解像度: 2.2→46.261 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.898 / 交差検証法: FREE R-VALUE / ESU R: 0.314 / ESU R Free: 0.221 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2568 | 4438 | 4.949 % |
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Rwork | 0.232 | 85230 | - |
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all | 0.233 | - | - |
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obs | - | 89668 | 99.936 % |
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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: 25.474 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.448 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -2.656 Å2 | 0 Å2 |
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3- | - | - | 3.105 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.2→46.261 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 12240 | 0 | 113 | 302 | 12655 |
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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_d0.002 | 0.012 | 12700 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.016 | 11414 | X-RAY DIFFRACTION | r_angle_refined_deg0.863 | 1.664 | 17356 | X-RAY DIFFRACTION | r_angle_other_deg0.54 | 1.582 | 26203 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.464 | 5 | 1570 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg4.976 | 5 | 108 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.719 | 10 | 1773 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg13.108 | 10 | 612 | X-RAY DIFFRACTION | r_chiral_restr0.047 | 0.2 | 1857 | X-RAY DIFFRACTION | r_gen_planes_refined0.003 | 0.02 | 15558 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 3050 | X-RAY DIFFRACTION | r_nbd_refined0.185 | 0.2 | 2771 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.209 | 0.2 | 10968 | X-RAY DIFFRACTION | r_nbtor_refined0.176 | 0.2 | 6257 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.078 | 0.2 | 6284 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.109 | 0.2 | 514 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.033 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.102 | 0.2 | 36 | X-RAY DIFFRACTION | r_nbd_other0.175 | 0.2 | 86 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.104 | 0.2 | 11 | X-RAY DIFFRACTION | r_mcbond_it0.41 | 2.65 | 6292 | X-RAY DIFFRACTION | r_mcbond_other0.41 | 2.65 | 6292 | X-RAY DIFFRACTION | r_mcangle_it0.772 | 4.765 | 7858 | X-RAY DIFFRACTION | r_mcangle_other0.772 | 4.766 | 7859 | X-RAY DIFFRACTION | r_scbond_it0.24 | 2.64 | 6408 | X-RAY DIFFRACTION | r_scbond_other0.24 | 2.64 | 6409 | X-RAY DIFFRACTION | r_scangle_it0.483 | 4.846 | 9498 | X-RAY DIFFRACTION | r_scangle_other0.483 | 4.846 | 9499 | X-RAY DIFFRACTION | r_lrange_it1.562 | 25.324 | 14420 | X-RAY DIFFRACTION | r_lrange_other1.562 | 25.324 | 14421 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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2.2-2.257 | 0.361 | 316 | 0.313 | 6231 | 0.315 | 6548 | 0.885 | 0.918 | 99.9847 | 0.287 | 2.257-2.319 | 0.339 | 322 | 0.3 | 6063 | 0.302 | 6386 | 0.905 | 0.927 | 99.9843 | 0.271 | 2.319-2.386 | 0.325 | 321 | 0.298 | 5865 | 0.299 | 6189 | 0.918 | 0.932 | 99.9515 | 0.268 | 2.386-2.459 | 0.321 | 250 | 0.288 | 5809 | 0.289 | 6062 | 0.905 | 0.938 | 99.9505 | 0.259 | 2.459-2.539 | 0.3 | 259 | 0.282 | 5572 | 0.283 | 5832 | 0.936 | 0.941 | 99.9828 | 0.252 | 2.539-2.628 | 0.296 | 261 | 0.262 | 5410 | 0.264 | 5674 | 0.934 | 0.95 | 99.9471 | 0.23 | 2.628-2.727 | 0.318 | 265 | 0.252 | 5183 | 0.255 | 5449 | 0.929 | 0.955 | 99.9817 | 0.224 | 2.727-2.838 | 0.286 | 258 | 0.245 | 5042 | 0.247 | 5300 | 0.945 | 0.958 | 100 | 0.219 | 2.838-2.964 | 0.302 | 288 | 0.245 | 4789 | 0.248 | 5080 | 0.936 | 0.958 | 99.9409 | 0.216 | 2.964-3.108 | 0.255 | 240 | 0.243 | 4604 | 0.243 | 4850 | 0.955 | 0.96 | 99.8763 | 0.22 | 3.108-3.275 | 0.276 | 238 | 0.244 | 4390 | 0.245 | 4628 | 0.953 | 0.96 | 100 | 0.221 | 3.275-3.473 | 0.244 | 222 | 0.236 | 4158 | 0.236 | 4383 | 0.964 | 0.965 | 99.9316 | 0.22 | 3.473-3.711 | 0.226 | 254 | 0.219 | 3878 | 0.219 | 4132 | 0.97 | 0.97 | 100 | 0.201 | 3.711-4.006 | 0.209 | 203 | 0.189 | 3652 | 0.19 | 3857 | 0.972 | 0.977 | 99.9481 | 0.172 | 4.006-4.385 | 0.179 | 184 | 0.181 | 3391 | 0.181 | 3578 | 0.982 | 0.98 | 99.9162 | 0.163 | 4.385-4.897 | 0.217 | 123 | 0.178 | 3125 | 0.179 | 3252 | 0.976 | 0.982 | 99.877 | 0.161 | 4.897-5.644 | 0.196 | 154 | 0.195 | 2728 | 0.195 | 2884 | 0.978 | 0.979 | 99.9306 | 0.176 | 5.644-6.887 | 0.22 | 139 | 0.189 | 2333 | 0.191 | 2472 | 0.976 | 0.979 | 100 | 0.169 | 6.887-9.634 | 0.164 | 84 | 0.162 | 1881 | 0.162 | 1967 | 0.981 | 0.983 | 99.8983 | 0.151 | 9.634-46.261 | 0.302 | 57 | 0.209 | 1126 | 0.213 | 1188 | 0.897 | 0.97 | 99.5791 | 0.206 |
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