ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | REFMAC | | 精密化 | | PDB_EXTRACT | 2 | データ抽出 | | HKL-2000 | | データ削減 | | 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: 1.95→14.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.849 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.228 | 1106 | 5.1 % | RANDOM |
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Rwork | 0.181 | - | - | - |
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all | 0.184 | 21687 | - | - |
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obs | 0.184 | 21614 | 99.66 % | - |
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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 |
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原子変位パラメータ | Biso mean: 24.859 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.01 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.02 Å2 | 0 Å2 |
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3- | - | - | -0.01 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→14.85 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2046 | 0 | 62 | 311 | 2419 |
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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_d0.016 | 0.022 | 2148 | X-RAY DIFFRACTION | r_angle_refined_deg1.491 | 2.001 | 2922 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.032 | 5 | 251 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.724 | 26.727 | 110 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.444 | 15 | 381 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.042 | 15 | 6 | X-RAY DIFFRACTION | r_chiral_restr0.109 | 0.2 | 328 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 1606 | X-RAY DIFFRACTION | r_nbd_refined0.225 | 0.2 | 1039 | X-RAY DIFFRACTION | r_nbtor_refined0.306 | 0.2 | 1495 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.149 | 0.2 | 241 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.194 | 0.2 | 45 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.144 | 0.2 | 19 | X-RAY DIFFRACTION | r_mcbond_it0.854 | 1.5 | 1310 | X-RAY DIFFRACTION | r_mcangle_it1.256 | 2 | 2065 | X-RAY DIFFRACTION | r_scbond_it2.19 | 3 | 1018 | X-RAY DIFFRACTION | r_scangle_it3.271 | 4.5 | 857 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.95→1.994 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.195 | 57 | - |
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Rwork | 0.176 | 1434 | - |
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obs | - | 1491 | 96.5 % |
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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 | 6.6357 | -9.5979 | -9.1249 | 22.3995 | 16.7697 | 14.0454 | 0.1781 | 1.05 | -0.3251 | -1.1973 | -0.6492 | 2.2568 | -0.4663 | -1.3086 | 0.4711 | 0.0803 | 0.0195 | -0.0536 | 0.1059 | 0.0811 | 0.2026 | 13.0635 | 30.1948 | -0.1273 | 2 | 0.8547 | 0.2923 | -0.1012 | 1.6626 | -0.115 | 1.3489 | 0.0423 | 0.0313 | -0.0161 | -0.0212 | -0.0129 | -0.0667 | -0.0417 | -0.0126 | -0.0294 | -0.0992 | -0.0053 | 0.0041 | -0.08 | 0.0013 | -0.0978 | 24.6019 | 28.9685 | 14.5327 | 3 | 16.2849 | -18.7814 | -1.9444 | 22.8112 | 2.8969 | 0.6044 | 0.1882 | 0.0512 | -0.103 | -0.292 | -0.272 | 0.6729 | -0.2162 | -0.12 | 0.0838 | 0.0994 | 0.0837 | -0.0383 | 0.0816 | 0.013 | 0.0867 | 4.9041 | 47.2879 | 5.4395 | 4 | 39.5086 | -26.3186 | 8.2594 | 57.2121 | 26.3281 | 37.2528 | -1.0245 | -1.4263 | 2.2431 | 1.8463 | 0.1799 | 0.6203 | -1.085 | -1.7042 | 0.8446 | 0.2622 | 0.0654 | 0.078 | 0.1342 | -0.0047 | 0.3669 | 3.3788 | 29.1044 | 12.0988 | 5 | 2.9252 | -0.8622 | -0.1971 | 2.4432 | 0.0016 | 1.3906 | 0.0316 | 0.1694 | 0.0091 | -0.0966 | -0.0375 | -0.1165 | 0.0519 | -0.0547 | 0.0059 | -0.0731 | -0.0021 | 0.0111 | -0.058 | -0.011 | -0.0786 | 11.3448 | 10.9789 | 9.2021 | 6 | 4.546 | -11.7425 | 0.0375 | 36.6645 | -1.8683 | 0.4957 | 1.2428 | 0.5448 | -0.0781 | -2.813 | -1.0335 | 0.5301 | -0.4247 | -0.0543 | -0.2093 | 0.4596 | 0.1691 | -0.0135 | 0.2447 | -0.0184 | 0.1151 | -2.0235 | 32.6517 | -0.569 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Selection: ALL ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | AA20 - 24 | 5 - 9 | 2 | 2 | AA25 - 125 | 10 - 110 | 3 | 3 | AA126 - 147 | 111 - 132 | 4 | 4 | BB20 - 24 | 5 - 9 | 5 | 5 | BB25 - 125 | 10 - 110 | 6 | 6 | BB126 - 144 | 111 - 129 | | | | | | | | | | | | |
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