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 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | HKL-3000 | | 位相決定 | SHELXE | | モデル構築 | SOLVE | | 位相決定 | RESOLVE | | 位相決定 | ARP/wARP | | モデル構築 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.56→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.929 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.326 / 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 | 0.26627 | 1197 | 5.1 % | RANDOM |
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Rwork | 0.21085 | - | - | - |
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obs | 0.21367 | 22126 | 98.08 % | - |
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all | - | 22126 | - | - |
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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: MASK |
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原子変位パラメータ | Biso mean: 76.237 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.68 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 1.68 Å2 | 0 Å2 |
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3- | - | - | -3.35 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.56→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4820 | 0 | 0 | 13 | 4833 |
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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_d0.02 | 0.022 | 4954 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.795 | 1.929 | 6728 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.503 | 5 | 610 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg42.957 | 24.754 | 244 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg19.264 | 15 | 794 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.902 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.125 | 0.2 | 744 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 3810 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.244 | 0.2 | 2335 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.32 | 0.2 | 3327 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.175 | 0.2 | 171 | 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_refined0.194 | 0.2 | 21 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.058 | 0.2 | 1 | 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_it0.921 | 1.5 | 3102 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.406 | 2 | 4865 | X-RAY DIFFRACTION | r_scbond_it2.318 | 3 | 2090 | X-RAY DIFFRACTION | r_scangle_it3.391 | 4.5 | 1861 | 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: 2.56→2.621 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.44 | 72 | - |
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Rwork | 0.327 | 1358 | - |
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obs | - | - | 83.87 % |
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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 | 3.0488 | -0.4569 | 1.7131 | 4.1825 | 0.4662 | 6.3666 | -0.3174 | 0.1294 | 0.1724 | 0.0847 | 0.2074 | 0.1339 | -0.6516 | -0.6504 | 0.11 | -0.2366 | 0.2005 | 0.049 | 0.1536 | -0.125 | -0.2851 | -3.21 | 38.279 | 5.87 | 2 | 1.9888 | -0.6205 | 1.3994 | 2.9151 | -0.8567 | 3.924 | -0.3862 | -0.4714 | 0.3429 | 0.4347 | 0.268 | 0.1443 | -0.3894 | -0.7944 | 0.1182 | -0.2815 | 0.189 | 0.0654 | -0.0116 | -0.1476 | -0.3621 | 3.698 | 32.041 | 23.394 | 3 | 2.711 | -0.6939 | 0.5528 | 2.891 | -0.5386 | 2.3426 | -0.0837 | -0.1463 | -0.0404 | 0.1246 | 0.1115 | 0.1757 | 0.1869 | -0.5328 | -0.0278 | -0.2372 | 0.0349 | 0.0632 | -0.0594 | -0.0588 | -0.3836 | 10.596 | 19.905 | 25.395 | 4 | 5.9489 | -0.8183 | 2.671 | 6.5949 | 0.0641 | 6.4765 | 0.2504 | -1.3221 | -0.7248 | 1.2095 | -0.1285 | -0.0475 | 0.9125 | -0.069 | -0.1219 | 0.4368 | 0.1501 | -0.1037 | 0.2654 | 0.0136 | -0.0114 | 41.269 | -1.666 | 44.95 | 5 | 2.6489 | -1.5029 | 1.2531 | 3.773 | 0.5192 | 3.9356 | -0.0954 | -0.1052 | -0.093 | 0.0324 | 0.2599 | -0.5308 | 0.5029 | 0.3094 | -0.1645 | -0.1518 | 0.0578 | 0.0498 | -0.1829 | -0.053 | -0.4079 | 33.376 | 3.701 | 27.693 | 6 | 3.0149 | -0.6103 | 0.549 | 4.2231 | 1.3599 | 4.0735 | -0.0409 | -0.4082 | -0.0343 | 0.333 | -0.0012 | 0.1838 | 0.4913 | -0.4297 | 0.042 | -0.137 | -0.0192 | 0.0372 | -0.1239 | -0.0222 | -0.4033 | 20.87 | 10.11 | 26.64 |
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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 - 119 | 1 - 119 | 2 | X-RAY DIFFRACTION | 2 | AA120 - 139 | 120 - 139 | 3 | X-RAY DIFFRACTION | 2 | AA172 - 192 | 172 - 192 | 4 | X-RAY DIFFRACTION | 2 | AA276 - 320 | 276 - 320 | 5 | X-RAY DIFFRACTION | 3 | AA140 - 153 | 140 - 153 | 6 | X-RAY DIFFRACTION | 3 | AA193 - 275 | 193 - 275 | 7 | X-RAY DIFFRACTION | 4 | BB1 - 119 | 1 - 119 | 8 | X-RAY DIFFRACTION | 5 | BB120 - 139 | 120 - 139 | 9 | X-RAY DIFFRACTION | 5 | BB172 - 192 | 172 - 192 | 10 | X-RAY DIFFRACTION | 5 | BB276 - 320 | 276 - 320 | 11 | X-RAY DIFFRACTION | 6 | BB140 - 153 | 140 - 153 | 12 | X-RAY DIFFRACTION | 6 | BB193 - 275 | 193 - 275 | | | | | | | | | | | | | | | | | | | | | | | | |
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