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 | MOLREP | | 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: TgalU-nat 解像度: 1.6→90.079 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.347 / SU ML: 0.072 / 交差検証法: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.082 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2037 | 4258 | 4.844 % |
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Rwork | 0.1762 | 83643 | - |
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all | 0.178 | - | - |
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obs | - | 87901 | 99.819 % |
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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: 30.66 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.359 Å2 | 0 Å2 | -1.1 Å2 |
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2- | - | -0.313 Å2 | 0 Å2 |
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3- | - | - | -0.887 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→90.079 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4371 | 0 | 148 | 479 | 4998 |
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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_d0.011 | 0.012 | 4729 | X-RAY DIFFRACTION | r_bond_other_d0.003 | 0.016 | 4506 | X-RAY DIFFRACTION | r_angle_refined_deg1.79 | 1.666 | 6403 | X-RAY DIFFRACTION | r_angle_other_deg0.671 | 1.562 | 10502 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.531 | 5 | 602 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg8.777 | 5 | 46 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.664 | 10 | 749 | X-RAY DIFFRACTION | r_dihedral_angle_other_3_deg24.433 | 10 | 3 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg16.909 | 10 | 207 | X-RAY DIFFRACTION | r_chiral_restr0.089 | 0.2 | 731 | X-RAY DIFFRACTION | r_chiral_restr_other0.1 | 0.2 | 3 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.02 | 5396 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 852 | X-RAY DIFFRACTION | r_nbd_refined0.207 | 0.2 | 896 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.164 | 0.2 | 4088 | X-RAY DIFFRACTION | r_nbtor_refined0.159 | 0.2 | 2189 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.073 | 0.2 | 2467 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.149 | 0.2 | 400 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.126 | 0.2 | 23 | X-RAY DIFFRACTION | r_nbd_other0.174 | 0.2 | 74 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.134 | 0.2 | 12 | X-RAY DIFFRACTION | r_mcbond_it2.146 | 2.228 | 2344 | X-RAY DIFFRACTION | r_mcbond_other2.116 | 2.227 | 2343 | X-RAY DIFFRACTION | r_mcangle_it3.05 | 3.33 | 2936 | X-RAY DIFFRACTION | r_mcangle_other3.05 | 3.33 | 2937 | X-RAY DIFFRACTION | r_scbond_it3.247 | 2.655 | 2385 | X-RAY DIFFRACTION | r_scbond_other3.246 | 2.656 | 2386 | X-RAY DIFFRACTION | r_scangle_it4.723 | 3.811 | 3456 | X-RAY DIFFRACTION | r_scangle_other4.723 | 3.812 | 3457 | X-RAY DIFFRACTION | r_lrange_it7.075 | 46.378 | 19735 | X-RAY DIFFRACTION | r_lrange_other7.074 | 46.368 | 19732 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.6-1.642 | 0.304 | 325 | 0.303 | 6169 | 0.303 | 6501 | 0.925 | 0.928 | 99.8923 | 0.287 | 1.642-1.687 | 0.317 | 280 | 0.285 | 5956 | 0.286 | 6256 | 0.929 | 0.939 | 99.6803 | 0.265 | 1.687-1.735 | 0.314 | 257 | 0.263 | 5912 | 0.265 | 6175 | 0.929 | 0.948 | 99.9028 | 0.239 | 1.735-1.789 | 0.25 | 268 | 0.25 | 5712 | 0.25 | 5984 | 0.957 | 0.957 | 99.9332 | 0.221 | 1.789-1.847 | 0.239 | 269 | 0.223 | 5536 | 0.224 | 5817 | 0.965 | 0.966 | 99.7937 | 0.194 | 1.847-1.912 | 0.249 | 259 | 0.206 | 5332 | 0.208 | 5599 | 0.962 | 0.972 | 99.8571 | 0.178 | 1.912-1.984 | 0.238 | 262 | 0.205 | 5107 | 0.206 | 5373 | 0.965 | 0.973 | 99.9256 | 0.181 | 1.984-2.065 | 0.211 | 259 | 0.181 | 4969 | 0.183 | 5231 | 0.971 | 0.979 | 99.9426 | 0.164 | 2.065-2.157 | 0.226 | 251 | 0.181 | 4730 | 0.184 | 4987 | 0.969 | 0.98 | 99.8797 | 0.165 | 2.157-2.262 | 0.221 | 268 | 0.177 | 4513 | 0.179 | 4788 | 0.97 | 0.981 | 99.8538 | 0.164 | 2.262-2.385 | 0.206 | 217 | 0.171 | 4331 | 0.173 | 4563 | 0.975 | 0.981 | 99.6713 | 0.16 | 2.385-2.529 | 0.202 | 227 | 0.166 | 4090 | 0.168 | 4319 | 0.975 | 0.983 | 99.9537 | 0.158 | 2.529-2.704 | 0.189 | 181 | 0.163 | 3846 | 0.165 | 4040 | 0.977 | 0.984 | 99.6782 | 0.158 | 2.704-2.92 | 0.213 | 226 | 0.166 | 3523 | 0.169 | 3763 | 0.973 | 0.984 | 99.628 | 0.166 | 2.92-3.198 | 0.201 | 158 | 0.176 | 3321 | 0.178 | 3486 | 0.974 | 0.981 | 99.7992 | 0.18 | 3.198-3.575 | 0.198 | 144 | 0.169 | 2974 | 0.17 | 3128 | 0.976 | 0.984 | 99.6803 | 0.176 | 3.575-4.128 | 0.182 | 120 | 0.148 | 2683 | 0.15 | 2806 | 0.983 | 0.987 | 99.8931 | 0.162 | 4.128-5.052 | 0.158 | 115 | 0.138 | 2233 | 0.139 | 2356 | 0.988 | 0.989 | 99.6604 | 0.16 | 5.052-7.134 | 0.214 | 119 | 0.18 | 1723 | 0.182 | 1851 | 0.976 | 0.985 | 99.5138 | 0.2 | 7.134-90.079 | 0.133 | 53 | 0.177 | 984 | 0.174 | 1038 | 0.99 | 0.977 | 99.9037 | 0.206 |
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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 | 0.2953 | 0.0329 | 0.2068 | 1.6652 | 0.9686 | 1.7358 | 0.0004 | -0.0511 | 0.0279 | 0.0709 | -0.0052 | -0.1211 | 0.0728 | 0.0906 | 0.0048 | 0.0118 | 0.0029 | -0.0073 | 0.0241 | 0.0023 | 0.0166 | -17.8389 | -1.4961 | 33.3882 | 2 | 0.3965 | 0.0473 | -0.0441 | 0.8011 | 0.9743 | 1.7344 | 0.043 | 0.1182 | -0.0371 | -0.036 | 0.0868 | -0.1549 | 0.0407 | 0.1623 | -0.1298 | 0.1036 | 0.0263 | -0.0064 | 0.0562 | -0.0167 | 0.0416 | -15.8188 | -29.9963 | 12.5636 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLALLA9 - 299 | 2 | X-RAY DIFFRACTION | 1 | | ALLB9 - 299 | | | | | |
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