ソフトウェア | 名称: REFMAC / バージョン: 5.2.0005 / 分類: 精密化 |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.05→28.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.512 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.193 / 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 | 0.22514 | 1032 | 5.1 % | RANDOM |
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Rwork | 0.15064 | - | - | - |
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all | 0.15436 | - | - | - |
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obs | 0.15436 | 19146 | 94.1 % | - |
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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: 27.082 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.15 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.24 Å2 | 0 Å2 |
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3- | - | - | -0.09 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.05→28.52 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2733 | 0 | 23 | 273 | 3029 |
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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_d0.017 | 0.022 | 2890 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 2794 | X-RAY DIFFRACTION | r_angle_refined_deg1.793 | 2.017 | 3925 | X-RAY DIFFRACTION | r_angle_other_deg0.965 | 3 | 6495 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.526 | 5 | 356 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.104 | 23.689 | 122 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.617 | 15 | 514 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.205 | 15 | 24 | X-RAY DIFFRACTION | r_chiral_restr0.107 | 0.2 | 462 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 3143 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 562 | X-RAY DIFFRACTION | r_nbd_refined0.2 | 0.2 | 555 | X-RAY DIFFRACTION | r_nbd_other0.181 | 0.2 | 2734 | X-RAY DIFFRACTION | r_nbtor_refined0.169 | 0.2 | 1309 | X-RAY DIFFRACTION | r_nbtor_other0.087 | 0.2 | 1793 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.196 | 0.2 | 217 | X-RAY DIFFRACTION | r_xyhbond_nbd_other0.003 | 0.2 | 1 | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.22 | 0.2 | 15 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.3 | 0.2 | 100 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.277 | 0.2 | 19 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it1.007 | 1.5 | 1977 | X-RAY DIFFRACTION | r_mcbond_other0.233 | 1.5 | 732 | X-RAY DIFFRACTION | r_mcangle_it1.455 | 2 | 2903 | X-RAY DIFFRACTION | r_scbond_it2.338 | 3 | 1178 | X-RAY DIFFRACTION | r_scangle_it3.404 | 4.5 | 1022 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.05→2.101 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.283 | 61 | - |
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Rwork | 0.175 | 1217 | - |
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obs | - | - | 83.2 % |
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精密化 TLS | 手法: refined / Origin x: 11.915 Å / Origin y: 7.06 Å / Origin z: 51.172 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.1849 Å2 | -0.0119 Å2 | -0.0068 Å2 | - | -0.1351 Å2 | -0.0015 Å2 | - | - | -0.2042 Å2 |
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L | 0.8255 °2 | -0.1874 °2 | -0.1885 °2 | - | 0.8456 °2 | -0.0208 °2 | - | - | 0.7721 °2 |
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S | -0.0322 Å ° | -0.0412 Å ° | 0.0201 Å ° | 0.082 Å ° | -0.0008 Å ° | -0.0241 Å ° | -0.01 Å ° | 0.0689 Å ° | 0.033 Å ° |
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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 | AA2 - 180 | 2 - 180 | 2 | X-RAY DIFFRACTION | 1 | BB2 - 180 | 2 - 180 | 3 | X-RAY DIFFRACTION | 1 | BC1031 | 1 | | | | | | |
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