ソフトウェア | 名称 | バージョン | 分類 | NB |
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EPMR | 2.5 | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | MOSFLM | | データ削減 | | SCALEPACK | | データスケーリング | |
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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 2A8D 解像度: 2.301→29.37 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0 / SU B: 11.197 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.231 / 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 | 0.236 | 1990 | 9.8 % | RANDOM |
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Rwork | 0.191 | - | - | - |
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all | 0.195 | 20243 | - | - |
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obs | 0.195 | 20242 | 100 % | - |
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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: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso max: 103.42 Å2 / Biso mean: 44.069 Å2 / Biso min: 26.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.01 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.04 Å2 | 0 Å2 |
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3- | - | - | -0.03 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.301→29.37 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2920 | 0 | 22 | 138 | 3080 |
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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_d0.01 | 0.021 | 3006 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 1981 | X-RAY DIFFRACTION | r_angle_refined_deg1.158 | 1.939 | 4070 | X-RAY DIFFRACTION | r_angle_other_deg0.907 | 3.002 | 4821 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.317 | 5 | 366 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.348 | 24.043 | 141 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.17 | 15 | 515 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.837 | 15 | 18 | X-RAY DIFFRACTION | r_chiral_restr0.069 | 0.2 | 459 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 3308 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 604 | X-RAY DIFFRACTION | r_nbd_refined0.211 | 0.2 | 703 | X-RAY DIFFRACTION | r_nbd_other0.19 | 0.2 | 2065 | X-RAY DIFFRACTION | r_nbtor_refined0.171 | 0.2 | 1450 | X-RAY DIFFRACTION | r_nbtor_other0.087 | 0.2 | 1481 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.185 | 0.2 | 146 | X-RAY DIFFRACTION | r_xyhbond_nbd_other0.051 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.16 | 0.2 | 22 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.194 | 0.2 | 76 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.155 | 0.2 | 19 | X-RAY DIFFRACTION | r_mcbond_it0.94 | 1.5 | 2365 | X-RAY DIFFRACTION | r_mcbond_other0.106 | 1.5 | 758 | X-RAY DIFFRACTION | r_mcangle_it1.067 | 2 | 2933 | X-RAY DIFFRACTION | r_scbond_it1.369 | 3 | 1364 | X-RAY DIFFRACTION | r_scangle_it1.863 | 4.5 | 1137 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.301→2.36 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.255 | 139 | - |
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Rwork | 0.186 | 1305 | - |
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all | - | 1444 | - |
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obs | - | - | 100 % |
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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 | 1.4544 | -0.0586 | -0.2726 | 0.5969 | -0.3993 | 1.1751 | -0.0316 | 0.1736 | -0.122 | -0.1132 | 0.0044 | -0.0217 | 0.113 | -0.0083 | 0.0272 | -0.0167 | -0.0014 | 0.0203 | -0.0311 | -0.0254 | -0.0389 | 32.99 | 60.863 | 17.183 | 2 | 1.6454 | -0.4138 | -0.1835 | 1.2978 | -0.2595 | 1.0777 | 0.0144 | -0.0098 | 0.1285 | -0.0019 | 0.0203 | -0.0193 | -0.1643 | -0.0518 | -0.0346 | -0.0083 | 0.024 | -0.01 | -0.087 | -0.0006 | -0.0231 | 26.638 | 83.481 | 33.183 |
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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 | A35 - 220 | 2 | X-RAY DIFFRACTION | 2 | B35 - 216 | | |
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