ソフトウェア | 名称 | バージョン | 分類 | NB |
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SOLVE | 2.02 | 位相決定 | | RESOLVE | 2.02 | 位相決定 | | REFMAC | refmac_5.1.24精密化 | | DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PDB_EXTRACT | 1 | データ抽出 | | |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.1→34.922 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.249 / SU ML: 0.114 / SU R Cruickshank DPI: 0.181 / 交差検証法: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.17
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2326 | 4592 | 5.009 % | RANDOM |
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Rwork | 0.1803 | - | - | - |
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all | 0.183 | - | - | - |
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obs | 0.1829 | 87085 | 99.98 % | - |
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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: BABINET MODEL PLUS MASK |
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原子変位パラメータ | Biso mean: 30.501 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.008 Å2 | -0.004 Å2 | 0 Å2 |
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2- | - | -0.008 Å2 | 0 Å2 |
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3- | - | - | 0.011 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→34.922 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9546 | 0 | 0 | 645 | 10191 |
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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_d0.023 | 0.021 | 9770 | X-RAY DIFFRACTION | r_angle_refined_deg1.777 | 1.948 | 13236 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.716 | 5 | 1188 | X-RAY DIFFRACTION | r_chiral_restr0.138 | 0.2 | 1491 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.02 | 7346 | X-RAY DIFFRACTION | r_nbd_refined0.21 | 0.2 | 4278 | X-RAY DIFFRACTION | r_nbtor_refined0.317 | 0.2 | 6709 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.141 | 0.2 | 653 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.205 | 0.2 | 36 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.171 | 0.2 | 12 | X-RAY DIFFRACTION | r_mcbond_it1.982 | 2 | 5943 | X-RAY DIFFRACTION | r_mcangle_it3.569 | 4 | 9555 | X-RAY DIFFRACTION | r_scbond_it5.826 | 6 | 3827 | X-RAY DIFFRACTION | r_scangle_it8.029 | 8 | 3681 | | | | | | | | | | | | | | |
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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 | Num. reflection all | % reflection obs (%) |
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2.1-2.1544 | 0.303 | 316 | 0.235 | 6377 | 6703 | 99.85 | 2.154-2.2132 | 0.282 | 334 | 0.2 | 6186 | 6520 | | 2.213-2.2771 | 0.275 | 299 | 0.204 | 6038 | 6337 | | 2.277-2.3468 | 0.273 | 331 | 0.2 | 5827 | 6158 | | 2.347-2.4235 | 0.267 | 296 | 0.195 | 5686 | 5982 | | 2.423-2.5081 | 0.252 | 290 | 0.184 | 5478 | 5768 | | 2.508-2.6022 | 0.247 | 287 | 0.178 | 5333 | 5620 | | 2.602-2.7079 | 0.294 | 271 | 0.189 | 5114 | 5385 | | 2.708-2.8275 | 0.237 | 234 | 0.177 | 4965 | 5199 | | 2.828-2.9645 | 0.243 | 252 | 0.183 | 4678 | 4930 | | 2.965-3.1237 | 0.244 | 243 | 0.191 | 4488 | 4731 | | 3.124-3.3115 | 0.238 | 231 | 0.185 | 4264 | 4495 | | 3.311-3.5378 | 0.215 | 214 | 0.176 | 4012 | 4227 | | 3.538-3.818 | 0.235 | 194 | 0.18 | 3743 | 3939 | | 3.818-4.1775 | 0.181 | 185 | 0.146 | 3480 | 3665 | | 4.177-4.6622 | 0.161 | 189 | 0.142 | 3111 | 3300 | | 4.662-5.3675 | 0.202 | 137 | 0.156 | 2809 | 2946 | | 5.368-6.5354 | 0.275 | 124 | 0.193 | 2409 | 2534 | | 6.535-9.0847 | 0.211 | 101 | 0.186 | 1904 | 2005 | | 9.085-34.9215 | 0.207 | 64 | 0.212 | 1183 | 1247 | |
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