ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | CBASS | | データ収集 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | REFMAC | | 位相決定 | |
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精密化 | 構造決定の手法: refmac 開始モデル: pdb entry 3DIL 解像度: 2.5→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.872 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.477 / ESU R Free: 0.298 / 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 | 0.26788 | 1095 | 5.1 % | RANDOM |
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Rwork | 0.21151 | - | - | - |
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all | 0.21423 | 20868 | - | - |
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obs | 0.21423 | 20432 | 97.91 % | - |
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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: 32.023 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.57 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -4.24 Å2 | 0 Å2 |
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3- | - | - | 5.81 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.221 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.5→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 3752 | 28 | 83 | 3863 |
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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_d0.006 | 0.021 | 4209 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.254 | 3 | 6569 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_2_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_3_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_4_deg | | | X-RAY DIFFRACTION | r_chiral_restr0.065 | 0.2 | 870 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1834 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.163 | 0.2 | 1548 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.265 | 0.2 | 2614 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.126 | 0.2 | 216 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined0.153 | 0.2 | 5 | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.153 | 0.2 | 33 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.151 | 0.2 | 10 | 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_it0.262 | 1.5 | 5 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.276 | 2 | 7 | X-RAY DIFFRACTION | r_scbond_it0.638 | 3 | 4446 | X-RAY DIFFRACTION | r_scangle_it0.946 | 4.5 | 6562 | 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: 2.5→2.564 Å / Rfactor Rfree error: 0.298 / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.408 | 83 | - |
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Rwork | 0.356 | 1457 | - |
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obs | - | 1540 | 97.35 % |
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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 | 1.2704 | 1.1253 | 0.8257 | 3.3236 | -0.6701 | 2.4566 | 0.0346 | 0.2292 | -0.2268 | -0.3307 | 0.0494 | -0.0902 | 0.3361 | -0.2091 | -0.084 | -0.034 | 0.0256 | -0.0342 | -0.0321 | 0.0005 | -0.1759 | 29.8536 | -1.862 | 18.9924 | 2 | 0.7263 | -0.0046 | 0.0503 | 0.3766 | 0.2541 | 0.6062 | -0.0563 | 0.1133 | 0.4009 | -0.0308 | -0.0552 | 0.0888 | -0.2814 | -0.2223 | 0.1115 | 0.0615 | 0.0829 | -0.0406 | 0.0118 | 0.029 | 0.0584 | 7.3559 | 47.2894 | 21.1976 | 3 | 1.9781 | -0.8823 | 0.6919 | 0.4464 | -0.4838 | 0.9161 | 0.0698 | 0.1833 | -0.0388 | 0.0035 | -0.0726 | 0.191 | -0.1889 | -0.0463 | 0.0027 | -0.0251 | 0.0593 | -0.0553 | -0.0154 | -0.0159 | -0.0869 | 8.8636 | 27.1939 | 11.3035 | 4 | 2.619 | -1.7188 | 0.3304 | 1.8204 | -0.0703 | 0.858 | 0.1829 | 0.4452 | 0.4021 | -0.1332 | -0.2871 | -0.3833 | -0.1217 | 0.0197 | 0.1043 | -0.0456 | 0.0216 | -0.0168 | -0.0492 | 0.0618 | -0.113 | 29.9915 | 33.6243 | 15.426 | 5 | 4.0449 | 0.4055 | -0.2553 | 1.6463 | 0.3956 | 0.7731 | -0.0966 | -0.0573 | -0.4854 | 0.2287 | -0.0592 | -0.3341 | 0.1135 | 0.1743 | 0.1558 | -0.076 | 0.039 | -0.0232 | 0.0281 | 0.0529 | 0.0655 | 50.7391 | 8.6419 | 16.0099 |
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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 | AA1 - 11 | 1 - 11 | 2 | X-RAY DIFFRACTION | 1 | AA163 - 174 | 163 - 174 | 3 | X-RAY DIFFRACTION | 2 | AA12 - 79 | 12 - 79 | 4 | X-RAY DIFFRACTION | 3 | AA80 - 113 | 80 - 113 | 5 | X-RAY DIFFRACTION | 4 | AA114 - 140 | 114 - 140 | 6 | X-RAY DIFFRACTION | 5 | AA141 - 162 | 141 - 162 | | | | | | | | | | | | |
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