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 | ADSC | Quantumデータ収集 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | MOLREP | | 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 2BVJ 解像度: 1.95→38.75 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.318 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 / 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 | 0.21065 | 2874 | 5.1 % | RANDOM |
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Rwork | 0.18965 | - | - | - |
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obs | 0.19072 | 53921 | 99.84 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 32.769 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.01 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.01 Å2 | 0 Å2 |
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3- | - | - | -0.01 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.107 Å | 0.113 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→38.75 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3019 | 0 | 43 | 487 | 3549 |
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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_d0.016 | 0.022 | 3130 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.604 | 2.01 | 4269 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.078 | 5 | 388 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.931 | 23.129 | 147 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.363 | 15 | 497 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.716 | 15 | 32 | X-RAY DIFFRACTION | r_chiral_restr0.121 | 0.2 | 478 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 2420 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.227 | 0.2 | 1658 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.308 | 0.2 | 2175 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.187 | 0.2 | 433 | 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_refined0.307 | 0.2 | 43 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.188 | 0.2 | 23 | 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_it1.016 | 1.5 | 2003 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.537 | 2 | 3124 | X-RAY DIFFRACTION | r_scbond_it2.472 | 3 | 1255 | X-RAY DIFFRACTION | r_scangle_it3.784 | 4.5 | 1144 | 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: 1.95→2 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.238 | 202 | - |
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Rwork | 0.206 | 3932 | - |
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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 | 2.8205 | 0.8665 | -0.4097 | 1.394 | -0.1771 | 1.5222 | -0.0111 | 0.1175 | -0.1784 | -0.0827 | 0.0753 | -0.0838 | 0.0538 | 0.2456 | -0.0642 | -0.0497 | 0.0469 | -0.0008 | 0.1336 | -0.043 | 0.0815 | 10.4056 | 18.7883 | 23.8128 | 2 | 1.4101 | 0.1026 | 0.2657 | 1.6394 | -0.4895 | 3.7015 | -0.0202 | 0.2572 | -0.2108 | -0.0667 | -0.1317 | -0.0212 | 0.2658 | -0.1143 | 0.1519 | 0.0026 | 0.0149 | 0.0247 | 0.1421 | -0.0638 | 0.0937 | -13.3037 | 7.0219 | 15.57 | 3 | 39.1507 | -44.6297 | -8.6436 | 52.5949 | 14.5103 | 14.5213 | 1.5688 | -2.2803 | 1.0398 | -1.8807 | -0.1808 | -1.2623 | 0.0537 | 0.1579 | -1.388 | 0.3243 | 0.0028 | -0.0052 | 0.3145 | 0.0009 | 0.3212 | 1.2207 | -4.157 | 13.7202 | 4 | 1.0896 | -0.2637 | -0.221 | 0.6967 | 0.183 | 2.9722 | -0.0117 | 0.3085 | -0.1112 | -0.1422 | -0.1112 | 0.033 | 0.207 | -0.0863 | 0.1229 | 0.0382 | 0.0119 | 0.0129 | 0.1381 | -0.0378 | 0.0965 | -10.7859 | 8.501 | 14.3592 | 5 | 2.5125 | 1.245 | -1.0387 | 1.0946 | -0.6972 | 1.7783 | 0.018 | 0.0196 | 0.1442 | 0.0561 | 0.071 | 0.0263 | -0.0898 | 0.0957 | -0.089 | -0.0078 | 0.037 | 0.0039 | 0.1056 | -0.0252 | 0.0779 | 3.3092 | 22.1914 | 27.7553 | 6 | 1.4407 | 0.1778 | 0.1828 | 1.4811 | 0.2501 | 1.935 | -0.0135 | -0.1602 | -0.3081 | 0.0873 | -0.0811 | -0.1446 | 0.4845 | -0.0105 | 0.0945 | 0.0056 | 0.0341 | 0.0352 | 0.0555 | 0.0183 | 0.062 | -6.6918 | 4.2497 | 30.0698 |
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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 | AA7 - 78 | 7 - 78 | 2 | X-RAY DIFFRACTION | 2 | AA83 - 168 | 83 - 168 | 3 | X-RAY DIFFRACTION | 3 | AA169 - 180 | 169 - 180 | 4 | X-RAY DIFFRACTION | 4 | AA181 - 271 | 181 - 271 | 5 | X-RAY DIFFRACTION | 5 | AA272 - 343 | 272 - 343 | 6 | X-RAY DIFFRACTION | 6 | AA344 - 400 | 344 - 400 | | | | | | | | | | | | |
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