ソフトウェア | 名称 | バージョン | 分類 |
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BUSTER | 2.10.2精密化 | XDS | | データ削減 | XDS | | データスケーリング | 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: 4YMX 解像度: 1.84→33.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.19 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.16
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.252 | 1687 | 5 % | RANDOM |
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Rwork | 0.218 | - | - | - |
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obs | 0.219 | 33754 | 96.5 % | - |
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原子変位パラメータ | Biso mean: 42.77 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.82 Å2 | 0 Å2 | -0.6537 Å2 |
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2- | - | -9.3012 Å2 | 0 Å2 |
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3- | - | - | 4.4812 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.29 Å |
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精密化ステップ | サイクル: 1 / 解像度: 1.84→33.83 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3647 | 0 | 84 | 213 | 3944 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.009 | 3797 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg1.02 | 5123 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 1263 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_incorr_chiral_ct | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_trig_c_planes | 90 | HARMONIC2 | X-RAY DIFFRACTION | t_gen_planes | 554 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 3797 | HARMONIC20 | X-RAY DIFFRACTION | t_nbd | 0 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_omega_torsion2.8 | | | | X-RAY DIFFRACTION | t_other_torsion17.54 | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 488 | 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_contact | 4745 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.84→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
| Rfactor | 反射数 | %反射 |
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Rfree | 0.242 | 105 | 4.96 % |
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Rwork | 0.246 | 2010 | - |
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all | 0.246 | 2115 | - |
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obs | - | - | 69.71 % |
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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 | 2.74 | 0.2723 | -0.3468 | 2.8828 | -0.863 | 2.8328 | 0.0794 | 0.0723 | -0.1236 | 0.0261 | 0.011 | 0.0833 | -0.0622 | -0.1387 | -0.0904 | -0.0391 | 0.0058 | -0.0559 | -0.1452 | -0.0246 | -0.1874 | -18.414 | -7.858 | -46.6831 | 2 | 1.9069 | -0.4458 | -1.3393 | 4.7967 | -2.5772 | 5.0065 | 0.1648 | 0.4265 | -0.1212 | 0.0729 | 0.0261 | 0.4542 | -0.1341 | -0.4692 | -0.1908 | -0.1362 | 0.0288 | -0.0328 | -0.1152 | -0.0211 | -0.2459 | -6.9549 | -7.5904 | -5.6459 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | { A|* }2 | X-RAY DIFFRACTION | 2 | { B|* } | |
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