ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | PHENIX | 1.19.1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 / 解像度: 1.35→38.239 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.824 / SU ML: 0.033 / 交差検証法: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1744 | 1319 | 4.922 % |
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Rwork | 0.1304 | 25477 | - |
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all | 0.133 | - | - |
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obs | - | 26796 | 99.989 % |
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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: 22.737 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.881 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -0.44 Å2 | 0 Å2 |
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3- | - | - | -0.441 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.35→38.239 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 978 | 0 | 13 | 93 | 1084 |
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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_d0.014 | 0.012 | 1054 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.018 | 888 | X-RAY DIFFRACTION | r_angle_refined_deg1.621 | 1.639 | 1434 | X-RAY DIFFRACTION | r_angle_other_deg0.577 | 1.569 | 2015 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.795 | 5 | 138 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg30.852 | 22 | 60 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.769 | 15 | 164 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.117 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.082 | 0.2 | 130 | X-RAY DIFFRACTION | r_gen_planes_refined0.013 | 0.02 | 1223 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 247 | X-RAY DIFFRACTION | r_nbd_refined0.386 | 0.2 | 177 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.204 | 0.2 | 847 | X-RAY DIFFRACTION | r_nbtor_refined0.2 | 0.2 | 492 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.087 | 0.2 | 576 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.159 | 0.2 | 56 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.431 | 0.2 | 17 | X-RAY DIFFRACTION | r_nbd_other0.202 | 0.2 | 48 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.31 | 0.2 | 9 | X-RAY DIFFRACTION | r_mcbond_it4.907 | 2.104 | 528 | X-RAY DIFFRACTION | r_mcbond_other4.72 | 2.069 | 520 | X-RAY DIFFRACTION | r_mcangle_it5.175 | 3.133 | 660 | X-RAY DIFFRACTION | r_mcangle_other5.104 | 3.109 | 657 | X-RAY DIFFRACTION | r_scbond_it5.148 | 2.365 | 526 | X-RAY DIFFRACTION | r_scbond_other5.143 | 2.364 | 527 | X-RAY DIFFRACTION | r_scangle_it6.079 | 3.412 | 770 | X-RAY DIFFRACTION | r_scangle_other6.075 | 3.411 | 771 | X-RAY DIFFRACTION | r_lrange_it5.598 | 38.822 | 4463 | X-RAY DIFFRACTION | r_lrange_other5.486 | 38.42 | 4387 | X-RAY DIFFRACTION | r_rigid_bond_restr9.416 | 3 | 1942 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.35-1.385 | 0.27 | 103 | 0.217 | 1871 | 0.22 | 1974 | 0.885 | 0.913 | 100 | 0.188 | 1.385-1.423 | 0.225 | 94 | 0.186 | 1791 | 0.188 | 1885 | 0.921 | 0.932 | 100 | 0.16 | 1.423-1.464 | 0.208 | 90 | 0.166 | 1755 | 0.168 | 1845 | 0.932 | 0.944 | 100 | 0.137 | 1.464-1.509 | 0.201 | 83 | 0.141 | 1711 | 0.144 | 1794 | 0.962 | 0.96 | 100 | 0.113 | 1.509-1.559 | 0.165 | 77 | 0.119 | 1676 | 0.121 | 1753 | 0.97 | 0.972 | 100 | 0.094 | 1.559-1.613 | 0.152 | 91 | 0.103 | 1597 | 0.106 | 1688 | 0.973 | 0.977 | 100 | 0.082 | 1.613-1.674 | 0.197 | 88 | 0.102 | 1525 | 0.107 | 1613 | 0.956 | 0.977 | 100 | 0.082 | 1.674-1.742 | 0.159 | 80 | 0.1 | 1513 | 0.103 | 1593 | 0.968 | 0.98 | 100 | 0.083 | 1.742-1.819 | 0.144 | 66 | 0.098 | 1438 | 0.1 | 1504 | 0.974 | 0.983 | 100 | 0.085 | 1.819-1.908 | 0.182 | 56 | 0.105 | 1384 | 0.108 | 1440 | 0.963 | 0.979 | 100 | 0.094 | 1.908-2.011 | 0.161 | 72 | 0.105 | 1314 | 0.108 | 1386 | 0.97 | 0.983 | 100 | 0.097 | 2.011-2.133 | 0.164 | 71 | 0.103 | 1237 | 0.105 | 1308 | 0.965 | 0.982 | 100 | 0.097 | 2.133-2.279 | 0.167 | 59 | 0.108 | 1195 | 0.111 | 1255 | 0.967 | 0.98 | 99.9203 | 0.106 | 2.279-2.461 | 0.176 | 57 | 0.114 | 1084 | 0.117 | 1141 | 0.967 | 0.979 | 100 | 0.115 | 2.461-2.695 | 0.174 | 54 | 0.13 | 1012 | 0.133 | 1066 | 0.967 | 0.975 | 100 | 0.134 | 2.695-3.011 | 0.168 | 59 | 0.138 | 920 | 0.14 | 979 | 0.972 | 0.974 | 100 | 0.145 | 3.011-3.473 | 0.136 | 38 | 0.127 | 826 | 0.127 | 864 | 0.978 | 0.98 | 100 | 0.144 | 3.473-4.245 | 0.146 | 34 | 0.133 | 715 | 0.134 | 749 | 0.981 | 0.98 | 100 | 0.159 | 4.245-5.967 | 0.184 | 29 | 0.149 | 565 | 0.151 | 594 | 0.968 | 0.977 | 100 | 0.183 | 5.967-38.239 | 0.307 | 18 | 0.25 | 348 | 0.253 | 368 | 0.929 | 0.935 | 99.4565 | 0.309 |
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