ソフトウェア | 名称 | バージョン | 分類 | NB |
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MOSFLM | | データ削減 | | SCALA | 3.2.19データスケーリング | | PHASER | | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | |
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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 2A8D 解像度: 2.55→33.98 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.79 / SU B: 25.918 / SU ML: 0.263 / SU R Cruickshank DPI: 0.662 / SU Rfree: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.633 / ESU R Free: 0.342 / 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 | 0.283 | 743 | 5 % | RANDOM |
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Rwork | 0.211 | - | - | - |
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all | 0.214 | 14808 | - | - |
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obs | 0.214 | 14808 | 95.15 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso max: 71.97 Å2 / Biso mean: 48.095 Å2 / Biso min: 31.13 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.08 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.19 Å2 | 0 Å2 |
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3- | - | - | -0.27 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.55→33.98 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2920 | 0 | 27 | 0 | 2947 |
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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_d0.013 | 0.021 | 3012 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 1972 | X-RAY DIFFRACTION | r_angle_refined_deg1.433 | 1.939 | 4084 | X-RAY DIFFRACTION | r_angle_other_deg0.944 | 3.002 | 4802 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.483 | 5 | 366 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg40.895 | 24 | 140 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg19.662 | 15 | 512 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.9 | 15 | 18 | X-RAY DIFFRACTION | r_chiral_restr0.077 | 0.2 | 458 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 3312 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 602 | X-RAY DIFFRACTION | r_nbd_refined0.234 | 0.2 | 728 | X-RAY DIFFRACTION | r_nbd_other0.199 | 0.2 | 2035 | X-RAY DIFFRACTION | r_nbtor_refined0.18 | 0.2 | 1427 | X-RAY DIFFRACTION | r_nbtor_other0.091 | 0.2 | 1597 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.24 | 0.2 | 71 | X-RAY DIFFRACTION | r_xyhbond_nbd_other0.037 | 0.2 | 3 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.152 | 0.2 | 16 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.274 | 0.2 | 42 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.101 | 0.2 | 4 | X-RAY DIFFRACTION | r_mcbond_it0.696 | 1.5 | 2346 | X-RAY DIFFRACTION | r_mcbond_other0.097 | 1.5 | 752 | X-RAY DIFFRACTION | r_mcangle_it0.876 | 2 | 2932 | X-RAY DIFFRACTION | r_scbond_it1.382 | 3 | 1381 | X-RAY DIFFRACTION | r_scangle_it2.077 | 4.5 | 1152 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.55→2.616 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.353 | 51 | - |
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Rwork | 0.268 | 817 | - |
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all | - | 868 | - |
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obs | - | - | 77.99 % |
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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 | 3.2335 | -0.5486 | 0.2541 | 2.323 | 0.8838 | 1.6349 | 0.002 | -0.0469 | -0.4769 | 0.1465 | 0.0143 | 0.1339 | 0.4002 | 0.093 | -0.0164 | -0.0219 | 0.0482 | 0.0118 | -0.1705 | 0.0273 | -0.0235 | -2.557 | -18.738 | -37.913 | 2 | 3.2188 | 0.3516 | 0.1456 | 1.2931 | 0.6863 | 2.602 | 0.0252 | -0.4043 | -0.1962 | 0.3414 | -0.0366 | -0.0043 | 0.2607 | 0.0593 | 0.0113 | -0.0465 | 0.022 | 0.0402 | -0.102 | 0.0356 | -0.0855 | -8.966 | -3.467 | -17.024 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA34 - 215 | 34 - 215 | 2 | X-RAY DIFFRACTION | 2 | BB34 - 219 | 34 - 219 | | | | |
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