ソフトウェア | 名称 | バージョン | 分類 |
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BLU-MAX | | データ収集 | PHASER | | 位相決定 | PHENIX | | モデル構築 | BUSTER | 2.8.0精密化 | XDS | | データ削減 | xia2 | | データ削減 | xia2 | | データスケーリング | PHENIX | | 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: pdb entry 1S7J 解像度: 1.76→23.12 Å / Cor.coef. Fo:Fc: 0.9662 / Cor.coef. Fo:Fc free: 0.9498 / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.19 | 1630 | 5.07 % | RANDOM |
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Rwork | 0.158 | - | - | - |
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all | 0.1597 | 33802 | - | - |
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obs | 0.158 | 32172 | - | - |
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原子変位パラメータ | Biso mean: 30.24 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.2868 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.2868 Å2 | 0 Å2 |
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3- | - | - | -0.5737 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.183 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.76→23.12 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2041 | 0 | 34 | 370 | 2445 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.01 | 2230 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg1.09 | 3040 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 1039 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_trig_c_planes | 62 | HARMONIC2 | X-RAY DIFFRACTION | t_gen_planes | 322 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 2204 | HARMONIC20 | X-RAY DIFFRACTION | t_nbd | 0 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_omega_torsion4.11 | | | | X-RAY DIFFRACTION | t_other_torsion2.55 | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 294 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_ideal_dist_contact | 2862 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.76→1.82 Å / Total num. of bins used: 16
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2491 | 145 | 4.95 % |
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Rwork | 0.2031 | 2782 | - |
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all | 0.2054 | 2927 | - |
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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 | 1.8098 | 0.1234 | 0.7576 | 0.6892 | 0.4693 | 0.3966 | -0.0785 | -0.0731 | 0.1441 | -0.0434 | 0.0046 | -0.1258 | -0.1053 | -0.054 | 0.0739 | -0.0629 | 0.0256 | 0.0094 | -0.0572 | -0.0018 | -0.0637 | 10.949 | 36.7604 | 63.8394 | 2 | 3.4739 | -0.3781 | -2.4577 | 0.7714 | 1.2302 | 2.8182 | -0.038 | 0.2649 | 0.0829 | -0.1191 | -0.0109 | -0.031 | -0.1184 | 0.1729 | 0.0489 | 0.0353 | 0.0068 | 0.0159 | 0.0848 | 0.0103 | -0.0052 | 23.7669 | 29.1925 | 51.1958 | 3 | 3.3296 | 0.744 | -0.7283 | 2.0293 | -1.0835 | 2.5692 | 0.0078 | 0.3404 | 0.2459 | -0.2106 | 0.0294 | -0.1299 | 0.0557 | 0.0183 | -0.0371 | 0.021 | 0.0108 | 0.0412 | 0.0385 | 0.0155 | 0.0273 | 17.2612 | 31.951 | 56.0585 | 4 | 1.3006 | -0.9993 | 0.067 | 2.6284 | 0.1816 | 1.3433 | -0.0483 | 0.0473 | 0.1211 | 0.0288 | -0.0264 | -0.164 | -0.0586 | 0.024 | 0.0747 | -0.0514 | 0.0094 | 0.0233 | -0.0418 | -0.011 | -0.0635 | 11.3543 | 36.7112 | 54.4799 | 5 | 2.5436 | -1.2907 | -0.2032 | 0.6823 | -0.6538 | 0.8225 | 0.1095 | 0.1864 | 0.0916 | -0.1004 | -0.1482 | -0.0012 | -0.1443 | -0.1264 | 0.0387 | -0.0048 | 0.0181 | 0.0055 | -0.03 | -0.0248 | 0.0068 | 3.404 | 41.4384 | 50.3394 | 6 | 1.5575 | -0.1061 | 0.7057 | 0.9148 | 1.113 | 1.15 | 0.0763 | 0.1623 | -0.3166 | -0.0701 | -0.0687 | -0.0185 | 0.3029 | -0.3251 | -0.0076 | 0.0223 | -0.0882 | 0.0022 | -0.0098 | -0.0265 | -0.0135 | -16.6622 | 19.2045 | 52.1205 | 7 | 3.696 | 0.3207 | 0.6152 | 0.1546 | 0.366 | 2.2669 | -0.0446 | -0.0529 | -0.4026 | -0.0063 | 0.1065 | 0.0297 | 0.3916 | -0.1265 | -0.0619 | -0.0357 | -0.039 | 0.0064 | -0.0508 | 0.0118 | -0.0103 | -14.5309 | 18.6097 | 58.6285 | 8 | 2.694 | -0.2181 | -1.0688 | 3.2198 | -0.1599 | 3.8741 | -0.0374 | -0.1247 | -0.4404 | -0.0471 | -0.0623 | -0.0723 | 0.4216 | 0.0336 | 0.0997 | -0.032 | -0.0284 | 0.0239 | -0.0141 | 0.0156 | -0.0037 | -9.5959 | 20.0709 | 64.3574 | 9 | 3.2348 | 0.2212 | 0.2817 | 1.5909 | -1.1952 | 1.9257 | -0.0385 | -0.007 | -0.1547 | -0.0565 | 0.0122 | -0.0565 | 0.1077 | 0.0191 | 0.0264 | -0.0381 | -0.0111 | 0.0191 | -0.0326 | -0.0132 | -0.0768 | -7.0515 | 27.6146 | 60.1746 | 10 | 2.1723 | 0.7128 | -0.5187 | 0.7309 | -0.278 | 1.8789 | 0.0193 | -0.065 | 0.1148 | 0.0336 | 0.0861 | 0.2421 | -0.1245 | -0.2693 | -0.1054 | -0.0435 | 0.0046 | 0.0218 | -0.0098 | -0.0158 | -0.0409 | -11.0495 | 37.1238 | 60.3797 | 11 | 6.5953 | 0.0152 | 3.0638 | 0.8417 | -0.2903 | 2.4932 | -0.113 | 0.0453 | 0.1201 | -0.1011 | 0.0513 | -0.0792 | -0.0139 | 0.0051 | 0.0616 | 0.0317 | -0.0177 | 0.0146 | -0.0408 | -0.0175 | 0.0158 | 7.9236 | 38.9521 | 58.9779 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | {A|1 - 24} | A1 - 24 | 2 | X-RAY DIFFRACTION | 2 | {A|25 - 35} | A25 - 35 | 3 | X-RAY DIFFRACTION | 3 | {A|36 - 54} | A36 - 54 | 4 | X-RAY DIFFRACTION | 4 | {A|55 - 88} | A55 - 88 | 5 | X-RAY DIFFRACTION | 5 | {A|89 - 114} | A89 - 114 | 6 | X-RAY DIFFRACTION | 6 | {A|115 - 126} | A115 - 126 | 7 | X-RAY DIFFRACTION | 7 | {A|127 - 148} | A127 - 148 | 8 | X-RAY DIFFRACTION | 8 | {A|149 - 181} | A149 - 181 | 9 | X-RAY DIFFRACTION | 9 | {A|182 - 212} | A182 - 212 | 10 | X-RAY DIFFRACTION | 10 | {A|213 - 237} | A213 - 237 | 11 | X-RAY DIFFRACTION | 11 | {A|238 - 258} | A238 - 258 | | | | | | | | | | | |
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