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 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | REFMAC | | 位相決定 | |
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精密化 | 構造決定の手法: フーリエ合成 / 解像度: 2.2→36.43 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.783 / SU ML: 0.148 / 交差検証法: FREE R-VALUE / ESU R: 0.272 / ESU R Free: 0.207 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2241 | 2425 | 5.062 % |
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Rwork | 0.1665 | 45480 | - |
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all | 0.169 | - | - |
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obs | - | 47905 | 99.919 % |
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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: 34.338 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.668 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.475 Å2 | 0 Å2 |
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3- | - | - | 1.143 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.2→36.43 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7424 | 0 | 57 | 232 | 7713 |
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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_d0.017 | 0.013 | 7692 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.017 | 7225 | X-RAY DIFFRACTION | r_angle_refined_deg2.097 | 1.64 | 10436 | X-RAY DIFFRACTION | r_angle_other_deg1.442 | 1.578 | 16641 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.407 | 5 | 935 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.378 | 21.443 | 402 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.005 | 15 | 1296 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.626 | 15 | 55 | X-RAY DIFFRACTION | r_chiral_restr0.098 | 0.2 | 982 | X-RAY DIFFRACTION | r_gen_planes_refined0.013 | 0.02 | 8594 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1798 | X-RAY DIFFRACTION | r_nbd_refined0.216 | 0.2 | 1657 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.19 | 0.2 | 6912 | X-RAY DIFFRACTION | r_nbtor_refined0.177 | 0.2 | 3702 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.092 | 0.2 | 3690 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.141 | 0.2 | 312 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.009 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.252 | 0.2 | 6 | X-RAY DIFFRACTION | r_nbd_other0.164 | 0.2 | 49 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.124 | 0.2 | 6 | X-RAY DIFFRACTION | r_mcbond_it1.756 | 2.436 | 3740 | X-RAY DIFFRACTION | r_mcbond_other1.756 | 2.436 | 3739 | X-RAY DIFFRACTION | r_mcangle_it2.518 | 3.644 | 4666 | X-RAY DIFFRACTION | r_mcangle_other2.518 | 3.644 | 4667 | X-RAY DIFFRACTION | r_scbond_it2.207 | 2.655 | 3952 | X-RAY DIFFRACTION | r_scbond_other2.192 | 2.653 | 3948 | X-RAY DIFFRACTION | r_scangle_it3.324 | 3.898 | 5767 | X-RAY DIFFRACTION | r_scangle_other3.298 | 3.894 | 5761 | X-RAY DIFFRACTION | r_lrange_it4.302 | 28.226 | 8677 | X-RAY DIFFRACTION | r_lrange_other4.291 | 28.165 | 8642 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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 | 0.28 | 160 | 0.222 | 3314 | 0.225 | 3482 | 0.876 | 0.892 | 99.7702 | 0.193 | 2.257-2.319 | 0.275 | 161 | 0.19 | 3249 | 0.194 | 3410 | 0.891 | 0.924 | 100 | 0.161 | 2.319-2.385 | 0.247 | 173 | 0.179 | 3102 | 0.183 | 3275 | 0.915 | 0.933 | 100 | 0.152 | 2.385-2.459 | 0.244 | 173 | 0.179 | 3043 | 0.183 | 3217 | 0.923 | 0.939 | 99.9689 | 0.152 | 2.459-2.539 | 0.248 | 145 | 0.174 | 2968 | 0.177 | 3113 | 0.923 | 0.939 | 100 | 0.146 | 2.539-2.627 | 0.263 | 153 | 0.182 | 2865 | 0.186 | 3018 | 0.914 | 0.935 | 100 | 0.156 | 2.627-2.726 | 0.248 | 145 | 0.182 | 2760 | 0.185 | 2905 | 0.923 | 0.937 | 100 | 0.153 | 2.726-2.837 | 0.253 | 134 | 0.183 | 2676 | 0.186 | 2810 | 0.913 | 0.936 | 100 | 0.155 | 2.837-2.962 | 0.271 | 154 | 0.174 | 2542 | 0.18 | 2697 | 0.912 | 0.94 | 99.9629 | 0.15 | 2.962-3.106 | 0.257 | 123 | 0.173 | 2484 | 0.177 | 2607 | 0.908 | 0.946 | 100 | 0.15 | 3.106-3.272 | 0.24 | 140 | 0.176 | 2330 | 0.18 | 2470 | 0.928 | 0.951 | 100 | 0.159 | 3.272-3.469 | 0.227 | 103 | 0.165 | 2228 | 0.167 | 2331 | 0.943 | 0.962 | 100 | 0.152 | 3.469-3.706 | 0.198 | 107 | 0.161 | 2106 | 0.162 | 2213 | 0.945 | 0.963 | 100 | 0.15 | 3.706-4 | 0.203 | 87 | 0.147 | 1980 | 0.149 | 2067 | 0.954 | 0.968 | 100 | 0.143 | 4-4.376 | 0.171 | 101 | 0.133 | 1812 | 0.135 | 1913 | 0.97 | 0.977 | 100 | 0.137 | 4.376-4.884 | 0.171 | 103 | 0.141 | 1647 | 0.143 | 1750 | 0.97 | 0.976 | 100 | 0.146 | 4.884-5.623 | 0.219 | 89 | 0.16 | 1460 | 0.164 | 1550 | 0.959 | 0.97 | 99.9355 | 0.157 | 5.623-6.846 | 0.196 | 76 | 0.161 | 1263 | 0.163 | 1339 | 0.959 | 0.967 | 100 | 0.161 | 6.846-9.515 | 0.204 | 58 | 0.14 | 1017 | 0.143 | 1075 | 0.961 | 0.979 | 100 | 0.146 | 9.515-36.43 | 0.229 | 39 | 0.197 | 630 | 0.199 | 669 | 0.968 | 0.973 | 100 | 0.21 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 0.5538 | -0.193 | -0.2168 | 0.571 | 0.1926 | 0.4165 | -0.0162 | -0.1162 | 0.0509 | 0.0451 | 0.0592 | -0.015 | 0.0186 | 0.0865 | -0.043 | 0.0263 | 0.0049 | 0.0096 | 0.0473 | -0.022 | 0.0159 | -25.6349 | 15.6038 | -27.6169 | 2 | 0.6215 | -0.1519 | -0.1478 | 0.8145 | 0.365 | 0.986 | -0.1372 | -0.1972 | -0.115 | 0.252 | 0.1318 | 0.0412 | 0.3054 | 0.1654 | 0.0054 | 0.18 | 0.1156 | 0.0363 | 0.0988 | 0.0434 | 0.0261 | -20.6654 | -9.3339 | -17.3922 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA2 - 476 | 2 | X-RAY DIFFRACTION | 1 | ALLA501 | 3 | X-RAY DIFFRACTION | 2 | ALLB1 - 477 | 4 | X-RAY DIFFRACTION | 2 | ALLB1000 | | | | | | | | |
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