ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | REFMAC | 5.5.0102精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | SBC-Collect | | データ収集 | | HKL-3000 | | データ削減 | | MOLREP | | 位相決定 | | HKL-3000 | | 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: PDB entry 1Q98 解像度: 1.8→43 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 6.975 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.137 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.242 | 3740 | 5 % | RANDOM |
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Rwork | 0.206 | - | - | - |
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all | 0.207 | 74115 | - | - |
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obs | 0.207 | 74115 | 98.33 % | - |
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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 max: 54.17 Å2 / Biso mean: 18.685 Å2 / Biso min: 2.95 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.75 Å2 | 0 Å2 | 0.53 Å2 |
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2- | - | -1.04 Å2 | 0 Å2 |
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3- | - | - | -0.56 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.8→43 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5616 | 0 | 13 | 761 | 6390 |
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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_d0.02 | 0.022 | 6083 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 4175 | X-RAY DIFFRACTION | r_angle_refined_deg1.732 | 1.972 | 8331 | X-RAY DIFFRACTION | r_angle_other_deg0.978 | 3 | 10185 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.182 | 5 | 781 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.101 | 23.312 | 311 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.805 | 15 | 1057 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.539 | 15 | 54 | X-RAY DIFFRACTION | r_chiral_restr0.11 | 0.2 | 934 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.021 | 6812 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1299 | X-RAY DIFFRACTION | r_mcbond_it1.115 | 1.5 | 3623 | X-RAY DIFFRACTION | r_mcbond_other0.394 | 1.5 | 1435 | X-RAY DIFFRACTION | r_mcangle_it1.894 | 2 | 5914 | X-RAY DIFFRACTION | r_scbond_it3.085 | 3 | 2460 | X-RAY DIFFRACTION | r_scangle_it4.745 | 4.5 | 2368 | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.799→1.846 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.423 | 231 | - |
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Rwork | 0.382 | 4307 | - |
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all | - | 4538 | - |
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obs | - | 4538 | 82.17 % |
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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 | 0.8317 | 0.211 | 0.312 | 1.2781 | -0.1814 | 1.1665 | -0.0299 | 0.0065 | 0.0012 | -0.0742 | 0.0104 | 0.0273 | -0.0263 | -0.0396 | 0.0195 | 0.0155 | 0.0109 | -0.0066 | 0.0148 | -0.009 | 0.0093 | 39.0402 | 31.6314 | 55.5421 | 2 | 0.9782 | -0.1307 | -0.5219 | 1.4989 | -0.1744 | 0.9522 | -0.002 | -0.0041 | -0.0145 | 0.0912 | -0.0332 | 0.075 | -0.0048 | -0.0095 | 0.0352 | 0.0177 | -0.0121 | 0.0079 | 0.0108 | -0.0071 | 0.0099 | 34.4933 | 28.1934 | 86.0226 | 3 | 0.9222 | 0.0301 | -0.4439 | 1.484 | 0.0485 | 0.8341 | 0.0094 | 0.0082 | -0.0035 | -0.0451 | -0.0368 | -0.0733 | -0.0092 | 0.0043 | 0.0274 | 0.0127 | 0.0117 | 0.0063 | 0.0121 | 0.0061 | 0.0113 | 57.2297 | 57.9814 | 52.9132 | 4 | 0.859 | -0.1925 | 0.3261 | 1.196 | 0.1819 | 1.0483 | -0.0308 | -0.0183 | 0.0053 | 0.0705 | 0.008 | -0.0269 | -0.0171 | 0.0442 | 0.0228 | 0.0211 | -0.0112 | -0.0047 | 0.0153 | 0.0078 | 0.007 | 52.7734 | 61.3335 | 83.4339 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A2 - 176 | 2 | X-RAY DIFFRACTION | 1 | A223 - 753 | 3 | X-RAY DIFFRACTION | 2 | B1 - 174 | 4 | X-RAY DIFFRACTION | 2 | B301 - 303 | 5 | X-RAY DIFFRACTION | 2 | B223 - 757 | 6 | X-RAY DIFFRACTION | 3 | C1 - 174 | 7 | X-RAY DIFFRACTION | 3 | C302 - 305 | 8 | X-RAY DIFFRACTION | 3 | C223 - 761 | 9 | X-RAY DIFFRACTION | 4 | D2 - 176 | 10 | X-RAY DIFFRACTION | 4 | D304 | 11 | X-RAY DIFFRACTION | 4 | D223 - 760 | | | | | | | | | | | |
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