ソフトウェア | 名称 | バージョン | 分類 |
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CBASS | | データ収集 | MOLREP | | 位相決定 | REFMAC | 5.2.0019精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3F2Q 解像度: 3.05→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 41.907 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.397 / 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 | 0.23176 | 382 | 4.6 % | RANDOM |
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Rwork | 0.19955 | - | - | - |
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all | 0.20105 | 7953 | - | - |
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obs | 0.20105 | 7869 | 98.94 % | - |
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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: 1.4 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 63.051 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.69 Å2 | 1.34 Å2 | 0 Å2 |
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2- | - | 2.69 Å2 | 0 Å2 |
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3- | - | - | -4.03 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.371 Å |
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精密化ステップ | サイクル: LAST / 解像度: 3.05→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 2340 | 45 | 2 | 2387 |
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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_d0.006 | 0.021 | 2653 | X-RAY DIFFRACTION | r_angle_refined_deg1.028 | 3 | 4132 | X-RAY DIFFRACTION | r_chiral_restr0.053 | 0.2 | 548 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1158 | X-RAY DIFFRACTION | r_nbd_refined0.172 | 0.2 | 1099 | X-RAY DIFFRACTION | r_nbtor_refined0.281 | 0.2 | 1638 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.173 | 0.2 | 78 | X-RAY DIFFRACTION | r_metal_ion_refined0.074 | 0.2 | 2 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.166 | 0.2 | 24 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.142 | 0.2 | 2 | X-RAY DIFFRACTION | r_scbond_it0.886 | 3 | 2831 | X-RAY DIFFRACTION | r_scangle_it1.472 | 4.5 | 4132 | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 3.05→3.128 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.34 | 28 | - |
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Rwork | 0.309 | 557 | - |
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obs | - | 585 | 97.18 % |
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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 | 3.6905 | 5.0394 | 1.6187 | 6.8812 | 2.2103 | 0.71 | -0.3151 | -2.2885 | -1.4653 | 0.4583 | -0.2217 | -0.0226 | 0.9836 | -0.5165 | 0.5368 | 1.5284 | -0.0023 | -0.0166 | 1.5899 | 0.3654 | 1.8564 | 2.654 | 27.206 | 14.692 | 2 | 4.2175 | -0.0743 | -2.3381 | 3.0408 | -0.503 | 6.969 | 0.0032 | 0.1657 | -0.1167 | -0.0955 | 0.0188 | -0.0907 | -0.1225 | 1.0856 | -0.022 | -0.5138 | 0.0013 | 0.0083 | -0.104 | -0.0543 | 0.5383 | 44.768 | 42.307 | 9.278 | 3 | 4.7906 | -1.4929 | 1.146 | 4.5024 | -0.2822 | 2.0447 | 0.1187 | -0.5296 | -0.1464 | 0.792 | 0.0848 | 0.2884 | -0.2192 | -0.6325 | -0.2035 | -0.2953 | 0.0387 | 0.0697 | -0.2468 | -0.017 | 0.4973 | 17.327 | 47.13 | 17.619 | 4 | 3.247 | -2.2767 | 2.978 | 4.1644 | 3.3673 | 14.3212 | -0.3323 | -1.4351 | -0.3852 | 2.217 | -0.1754 | 1.4024 | -1.4006 | 0.4205 | 0.5077 | 1.0216 | -0.2237 | 0.0614 | 0.5404 | 0.2491 | 1.2278 | 22.691 | 33.662 | 35.553 | 5 | 8.6668 | -3.3296 | 2.9524 | 5.8648 | -0.6644 | 3.9026 | -0.2743 | -0.4698 | 0.4769 | 0.747 | 0.1032 | 0.3077 | -1.006 | -0.3522 | 0.1711 | -0.1103 | 0.057 | 0.1017 | -0.3535 | -0.1124 | 0.5744 | 22.265 | 59.903 | 14.91 | 6 | 12.2229 | -0.8309 | -0.3046 | 1.1827 | 0.6867 | 3.0969 | 0.2012 | 0.2994 | -2.3279 | 0.0992 | -0.0315 | 0.564 | 0.0931 | -0.5306 | -0.1697 | -0.4159 | 0.0521 | -0.0694 | -0.1349 | 0.1062 | 1.0353 | 23.839 | 30.857 | 16.104 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | X1 - 9 | 2 | X-RAY DIFFRACTION | 2 | X10 - 30 | 3 | X-RAY DIFFRACTION | 3 | X31 - 48 | 4 | X-RAY DIFFRACTION | 4 | Y57 - 60 | 5 | X-RAY DIFFRACTION | 4 | X49 - 54 | 6 | X-RAY DIFFRACTION | 5 | Y61 - 84 | 7 | X-RAY DIFFRACTION | 6 | Y85 - 112 | | | | | | | |
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