ソフトウェア | 名称 | バージョン | 分類 | NB |
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d*TREK | 9.2Lデータスケーリング | | PHASER | | 位相決定 | | REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3 | データ抽出 | | CrystalClear | | データ収集 | | d*TREK | | データ削減 | | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1GOX 解像度: 1.65→30.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.116 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096 / 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 | 0.212 | 2244 | 5 % | RANDOM |
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Rwork | 0.181 | - | - | - |
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obs | 0.183 | 44620 | 98.78 % | - |
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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: 13.36 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.06 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.06 Å2 | 0 Å2 |
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3- | - | - | 0.12 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.65→30.8 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2801 | 0 | 36 | 232 | 3069 |
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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_d0.014 | 0.022 | 2897 | X-RAY DIFFRACTION | r_angle_refined_deg1.35 | 1.986 | 3926 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.14 | 5 | 363 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.834 | 23.607 | 122 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.427 | 15 | 514 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg13.865 | 15 | 24 | X-RAY DIFFRACTION | r_chiral_restr0.11 | 0.2 | 446 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 2155 | X-RAY DIFFRACTION | r_nbd_refined0.201 | 0.2 | 1523 | X-RAY DIFFRACTION | r_nbtor_refined0.305 | 0.2 | 1983 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.111 | 0.2 | 208 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.158 | 0.2 | 73 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.107 | 0.2 | 14 | X-RAY DIFFRACTION | r_mcbond_it0.844 | 1.5 | 1851 | X-RAY DIFFRACTION | r_mcangle_it1.208 | 2 | 2886 | X-RAY DIFFRACTION | r_scbond_it2.219 | 3 | 1216 | X-RAY DIFFRACTION | r_scangle_it3.496 | 4.5 | 1038 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.65→1.693 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.384 | 152 | - |
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Rwork | 0.322 | 2755 | - |
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all | - | 2907 | - |
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obs | - | - | 87.4 % |
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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 | 0.6395 | 0.5471 | 0.3183 | 1.0127 | 0.4161 | 0.4543 | 0.0435 | -0.0952 | -0.0062 | 0.1459 | -0.067 | 0.0154 | 0.051 | -0.0394 | 0.0235 | 0.0883 | 0.0077 | 0.0244 | 0.0848 | 0.0065 | 0.0135 | 14.771 | -11.793 | -11.635 | 2 | 0.8326 | 0.1332 | -0.1625 | 0.8196 | -0.1158 | 0.2757 | 0.0096 | 0.0142 | -0.1773 | 0.0842 | 0.0199 | -0.2547 | 0.0471 | 0.0666 | -0.0295 | 0.0613 | 0.0132 | -0.0189 | 0.0456 | 0.0034 | 0.0611 | 31.996 | -20.681 | -16.85 | 3 | 1.0182 | -0.5599 | -0.5673 | 1.7724 | 0.4299 | 1.1496 | -0.0189 | -0.2528 | 0.0968 | 0.2725 | 0.136 | -0.4649 | -0.014 | 0.2389 | -0.1171 | 0.0455 | -0.0106 | -0.057 | 0.0868 | -0.018 | 0.1041 | 38.069 | -6.061 | -11.347 | 4 | 0.5194 | 0.2623 | 0.0874 | 1.5947 | 0.2158 | 0.2665 | -0.0158 | 0.0785 | 0.0083 | -0.1862 | 0.0543 | -0.1977 | -0.0259 | 0.0664 | -0.0385 | 0.0569 | -0.0009 | 0.0241 | 0.0658 | -0.0013 | 0.0181 | 27.511 | -8.946 | -27.012 | 5 | 1.8782 | 0.5216 | 1.1837 | 1.1596 | 0.4194 | 2.2483 | 0.0293 | 0.0543 | -0.1364 | 0.0382 | -0.0039 | -0.0259 | 0.0804 | -0.0246 | -0.0254 | 0.0606 | 0.0034 | 0.0262 | 0.043 | 0.0071 | 0.0364 | 15.699 | -23.965 | -18.069 |
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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 | AA3 - 54 | 20 - 71 | 2 | X-RAY DIFFRACTION | 2 | AA55 - 140 | 72 - 157 | 3 | X-RAY DIFFRACTION | 3 | AA141 - 202 | 158 - 219 | 4 | X-RAY DIFFRACTION | 4 | AA203 - 315 | 220 - 332 | 5 | X-RAY DIFFRACTION | 5 | AA316 - 362 | 333 - 379 | | | | | | | | | | |
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