ソフトウェア | 名称 | バージョン | 分類 |
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MAR345 | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.2.0019精密化 | XDS | | データ削減 | XSCALE | | 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 2IGO 解像度: 2→29.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.792 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.139 / 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 | 0.19956 | 1990 | 4.6 % | RANDOM |
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Rwork | 0.15643 | - | - | - |
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all | 0.15842 | 41420 | - | - |
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obs | 0.15842 | 41420 | 99.89 % | - |
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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 mean: 11.138 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.29 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.29 Å2 | 0 Å2 |
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3- | - | - | 0.59 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2→29.2 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4517 | 0 | 65 | 307 | 4889 |
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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_d0.022 | 0.022 | 4702 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 3167 | X-RAY DIFFRACTION | r_angle_refined_deg1.861 | 1.963 | 6396 | X-RAY DIFFRACTION | r_angle_other_deg1.011 | 3 | 7715 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.875 | 5 | 572 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.606 | 24.509 | 224 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.618 | 15 | 754 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.494 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.196 | 0.2 | 695 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 5216 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 940 | X-RAY DIFFRACTION | r_nbd_refined0.224 | 0.2 | 929 | X-RAY DIFFRACTION | r_nbd_other0.214 | 0.2 | 3368 | X-RAY DIFFRACTION | r_nbtor_refined0.182 | 0.2 | 2320 | X-RAY DIFFRACTION | r_nbtor_other0.093 | 0.2 | 2353 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.139 | 0.2 | 244 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.258 | 0.2 | 27 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.231 | 0.2 | 83 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.16 | 0.2 | 20 | 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_it1.393 | 1.5 | 3649 | X-RAY DIFFRACTION | r_mcbond_other0.303 | 1.5 | 1146 | X-RAY DIFFRACTION | r_mcangle_it1.694 | 2 | 4653 | X-RAY DIFFRACTION | r_scbond_it2.843 | 3 | 2145 | X-RAY DIFFRACTION | r_scangle_it3.871 | 4.5 | 1743 | 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→2.108 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.227 | 285 | - |
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Rwork | 0.152 | 5906 | - |
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obs | - | - | 99.98 % |
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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 | 0.1016 | 0.0388 | -0.0095 | 0.0207 | 0.0096 | 0.0307 | -0.0088 | 0.0138 | -0.0105 | 0.0035 | 0.0162 | -0.0154 | -0.0127 | -0.0057 | -0.0074 | 0.0301 | -0.0026 | 0.0076 | 0.0421 | -0.0097 | 0.0233 | 61.7523 | 46.6278 | 35.8776 | 2 | 0.1933 | 0.0605 | 0 | 0.2246 | 0.1303 | 0.2249 | -0.0046 | 0.0633 | 0.0274 | -0.0314 | 0.0043 | 0.0065 | -0.0493 | 0.0163 | 0.0003 | 0.0317 | -0.0102 | 0.0104 | 0.0397 | 0.012 | 0.0065 | 69.0537 | 65.8446 | 29.0855 | 3 | 0.3533 | -0.1498 | -0.1889 | 0.2136 | 0.1907 | 0.2726 | -0.0235 | 0.0141 | -0.0902 | 0.0029 | 0.0301 | 0.006 | -0.0127 | 0.0546 | -0.0066 | 0.0146 | 0.0044 | 0.0124 | 0.034 | -0.0206 | 0.0427 | 77.1902 | 40.5691 | 30.3282 | 4 | 1.0383 | -0.4665 | -0.0974 | 0.2561 | -0.0177 | 0.214 | -0.0071 | 0.0451 | 0.0325 | -0.0091 | 0.0067 | -0.0083 | 0.0098 | -0.0349 | 0.0004 | 0.0188 | 0.0001 | -0.0072 | 0.0293 | 0.011 | 0.0228 | 52.8582 | 79.1742 | 46.4249 | 5 | 0.1346 | -0.0239 | -0.043 | 0.1227 | 0.1011 | 0.1809 | -0.0171 | 0.0104 | -0.0308 | 0.0059 | 0.0198 | -0.0229 | -0.0205 | 0.0218 | -0.0026 | 0.0163 | -0.0048 | 0.0091 | 0.0424 | -0.0115 | 0.029 | 77.2436 | 53.0477 | 37.7203 |
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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 | A46 - 169 | 2 | X-RAY DIFFRACTION | 2 | A170 - 286 | 3 | X-RAY DIFFRACTION | 3 | A287 - 365 | 4 | X-RAY DIFFRACTION | 4 | A366 - 473 | 5 | X-RAY DIFFRACTION | 5 | A474 - 618 | | | | | |
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