ソフトウェア | 名称 | バージョン | 分類 |
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BUSTER | | 精密化 | XDS | 20180126 | データ削減 | Aimless | 0.7.2データスケーリング | PHASER | 2.8.2位相決定 | PDB_EXTRACT | 3.24 | 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: 4DWG 解像度: 1.47→49.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.066 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.067
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.212 | 3365 | 4.9 % | RANDOM |
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Rwork | 0.187 | - | - | - |
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obs | 0.188 | 68734 | 100 % | - |
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原子変位パラメータ | Biso max: 115.7 Å2 / Biso mean: 36.75 Å2 / Biso min: 18.78 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.8028 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.8028 Å2 | 0 Å2 |
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3- | - | - | -1.6055 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.21 Å |
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精密化ステップ | サイクル: final / 解像度: 1.47→49.93 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2863 | 0 | 16 | 287 | 3166 |
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Biso mean | - | - | 46.29 | 45.46 | - |
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残基数 | - | - | - | - | 359 |
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拘束条件 | Refine-ID | タイプ | 数 | Restraint function | Weight | Dev ideal |
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X-RAY DIFFRACTION | t_dihedral_angle_d1032 | SINUSOIDAL2 | | X-RAY DIFFRACTION | t_trig_c_planes | | | | X-RAY DIFFRACTION | t_gen_planes506 | HARMONIC5 | | X-RAY DIFFRACTION | t_it2984 | HARMONIC20 | | X-RAY DIFFRACTION | t_nbd0 | SEMIHARMONIC5 | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion381 | SEMIHARMONIC5 | | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact3989 | SEMIHARMONIC4 | | X-RAY DIFFRACTION | t_bond_d2984 | HARMONIC2 | 0.01 | X-RAY DIFFRACTION | t_angle_deg4052 | HARMONIC2 | 0.91 | X-RAY DIFFRACTION | t_omega_torsion | | | 2.81 | X-RAY DIFFRACTION | t_other_torsion | | | 16.27 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.47→1.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1846 | 60 | 4.36 % |
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Rwork | 0.2028 | 1315 | - |
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all | 0.2021 | 1375 | - |
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obs | - | - | 98.75 % |
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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 | 2.0082 | -0.3015 | 0.4213 | 0.521 | -0.0632 | 0.4423 | -0.0953 | 0.0422 | 0.278 | 0.0016 | 0.0137 | -0.0753 | -0.0496 | 0.0521 | 0.0815 | 0.0185 | 0.0105 | 0.0027 | 0.0364 | 0.0167 | -0.0186 | -3.6736 | -14.5963 | -32.9479 | 2 | 1.6496 | -0.0928 | -0.3478 | 0.4784 | -0.0749 | 0.2707 | -0.0491 | -0.2742 | -0.0388 | 0.077 | 0.0255 | 0.0181 | 0.0664 | 0.043 | 0.0236 | 0.0569 | 0.0307 | 0.0105 | 0.1229 | -0.0033 | -0.0788 | -11.8369 | -26.35 | -18.4916 | 3 | 2.8662 | 0.1423 | -0.1933 | 0.6316 | 0.1069 | 1.2244 | 0.0335 | -0.2437 | 0.459 | 0.045 | 0.0058 | 0.1367 | -0.32 | -0.0403 | -0.0393 | 0.0141 | -0.0235 | -0.0005 | 0.0168 | -0.0399 | -0.1701 | -13.8199 | -14.0373 | -6.9222 |
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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 - A|142 } | A1 - 142 | 2 | X-RAY DIFFRACTION | 2 | { A|143 - A|231 } | A143 - 231 | 3 | X-RAY DIFFRACTION | 3 | { A|232 - A|360 } | A232 - 360 | | | |
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