ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | BUSTER-TNT | 2.10.2精密化 | PDB_EXTRACT | 3.2 | データ抽出 | XDS | | 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 開始モデル: Theoretical model of RNA generated with RNAcomposer 解像度: 2.32→40 Å / Cor.coef. Fo:Fc: 0.9576 / Cor.coef. Fo:Fc free: 0.9436 / SU R Cruickshank DPI: 0.99 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.257
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2274 | 491 | 3.99 % | RANDOM |
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Rwork | 0.1845 | - | - | - |
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obs | 0.1866 | 12303 | 93.83 % | - |
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原子変位パラメータ | Biso max: 138.83 Å2 / Biso mean: 59.05 Å2 / Biso min: 24.53 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.0225 Å2 | 0 Å2 | 5.3761 Å2 |
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2- | - | -1.8343 Å2 | 0 Å2 |
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3- | - | - | 3.8568 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.314 Å |
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精密化ステップ | サイクル: final / 解像度: 2.32→40 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 2426 | 4 | 184 | 2614 |
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Biso mean | - | - | 59.44 | 47.86 | - |
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残基数 | - | - | - | - | 114 |
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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_d649 | SINUSOIDAL2 | | X-RAY DIFFRACTION | t_trig_c_planes | | | | X-RAY DIFFRACTION | t_gen_planes129 | HARMONIC5 | | X-RAY DIFFRACTION | t_it3072 | HARMONIC20 | | X-RAY DIFFRACTION | t_nbd2 | SEMIHARMONIC5 | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion516 | 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_contact3234 | SEMIHARMONIC4 | | X-RAY DIFFRACTION | t_bond_d3072 | HARMONIC2 | 0.01 | X-RAY DIFFRACTION | t_angle_deg4793 | HARMONIC2 | 0.85 | X-RAY DIFFRACTION | t_omega_torsion | | | | X-RAY DIFFRACTION | t_other_torsion | | | 26.46 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.32→2.54 Å / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2737 | 73 | 3.01 % |
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Rwork | 0.214 | 2352 | - |
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all | 0.2158 | 2425 | - |
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obs | - | - | 78.31 % |
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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 | 2.7849 | -0.0993 | 0.1603 | 2.3966 | -1.0928 | 6.0813 | 0.1461 | 0.0495 | 0.0362 | 0.0209 | -0.1051 | -0.3994 | -0.0599 | 0.5787 | -0.041 | -0.2835 | -0.0354 | -0.032 | -0.189 | 0.0451 | -0.1142 | 7.0227 | 0.5331 | 33.6236 | 2 | 3.2522 | -0.3761 | -0.9732 | 2.5444 | -0.2737 | 3.0984 | 0.0676 | -0.176 | -0.3144 | 0.0335 | 0.0658 | 0.2066 | 0.1551 | -0.1523 | -0.1335 | -0.2431 | -0.0227 | -0.0436 | -0.2154 | 0.0095 | -0.1903 | -17.7189 | -0.276 | 34.4312 |
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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|24 - A|87 } | A24 - 87 | 2 | X-RAY DIFFRACTION | 2 | { B|24 - B|87 } | B24 - 87 | | |
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