ソフトウェア | 名称 | バージョン | 分類 | NB |
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REFMAC | 5.2.0005精密化 | | PDB_EXTRACT | 2 | データ抽出 | | CBASS | | データ収集 | | HKL-2000 | | データ削減 | | HKL-2000 | | 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 1xfh 解像度: 2.96→100 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 51.372 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.265 | 1728 | 4.9 % | RANDOM |
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Rwork | 0.236 | - | - | - |
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obs | 0.238 | 15137 | 69.28 % | - |
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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: 101.432 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.86 Å2 | 1.93 Å2 | 0 Å2 |
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2- | - | 3.86 Å2 | 0 Å2 |
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3- | - | - | -5.79 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.96→100 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8575 | 0 | 78 | 3 | 8656 |
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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_d0.017 | 0.022 | 8815 | X-RAY DIFFRACTION | r_angle_refined_deg1.849 | 1.985 | 12037 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.565 | 5 | 1197 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.627 | 23.718 | 234 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg22.652 | 15 | 1294 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.757 | 15 | 18 | X-RAY DIFFRACTION | r_chiral_restr0.101 | 0.2 | 1539 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 6321 | X-RAY DIFFRACTION | r_nbd_refined0.276 | 0.3 | 5967 | X-RAY DIFFRACTION | r_nbtor_refined0.349 | 0.5 | 6425 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.229 | 0.5 | 635 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.122 | 0.3 | 6 | X-RAY DIFFRACTION | r_mcbond_it1.092 | 2 | 6054 | X-RAY DIFFRACTION | r_mcangle_it1.834 | 3 | 9484 | X-RAY DIFFRACTION | r_scbond_it1.151 | 2 | 3062 | X-RAY DIFFRACTION | r_scangle_it1.553 | 3 | 2553 | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION Ens-ID | Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
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1 | A2837 | TIGHT POSITIONAL0.06 | 0.05 | 1 | B2837 | TIGHT POSITIONAL0.05 | 0.05 | 1 | C2837 | TIGHT POSITIONAL0.05 | 0.05 | 1 | A2837 | TIGHT THERMAL2.04 | 5 | 1 | B2837 | TIGHT THERMAL1.64 | 5 | 1 | C2837 | TIGHT THERMAL1.45 | 5 | 2 | A9 | TIGHT POSITIONAL0.03 | 0.05 | 2 | B9 | TIGHT POSITIONAL0.06 | 0.05 | 2 | C9 | TIGHT POSITIONAL0.04 | 0.05 | 2 | A9 | TIGHT THERMAL2.38 | 5 | 2 | B9 | TIGHT THERMAL3.11 | 5 | 2 | C9 | TIGHT THERMAL1.09 | 5 | 3 | A17 | TIGHT POSITIONAL0.07 | 0.05 | 3 | B17 | TIGHT POSITIONAL0.09 | 0.05 | 3 | C17 | TIGHT POSITIONAL0.04 | 0.05 | 3 | A17 | TIGHT THERMAL0.63 | 5 | 3 | B17 | TIGHT THERMAL2.16 | 5 | 3 | C17 | TIGHT THERMAL2.25 | 5 | 4 | A1 | TIGHT POSITIONAL | 0.05 | 4 | B1 | TIGHT POSITIONAL | 0.05 | 4 | C1 | TIGHT POSITIONAL | 0.05 | 4 | A1 | TIGHT THERMAL6.44 | 5 | 4 | B1 | TIGHT THERMAL8.87 | 5 | 4 | C1 | TIGHT THERMAL2.42 | 5 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.956→3.033 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.423 | 12 | - |
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Rwork | 0.366 | 316 | - |
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obs | - | 328 | 8.76 % |
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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 | 0.7188 | 0.5841 | 0.4282 | 1.9807 | 0.4099 | 2.402 | -0.205 | 0.1083 | 0.1379 | 0.1391 | 0.277 | -0.0109 | 0.2128 | 0.1715 | -0.072 | 0.1557 | 0.0871 | 0.0294 | 0.2247 | 0.0333 | -0.0686 | 12.0546 | 4.1907 | 13.663 | 2 | 1.152 | -0.5405 | -0.1146 | 1.5177 | -0.683 | 2.1658 | 0.065 | 0.2211 | 0.3344 | -0.3055 | 0.0841 | 0.2338 | -0.6749 | -0.1496 | -0.1491 | 0.6438 | 0.0841 | -0.0376 | 0.2946 | 0.1283 | 0.3231 | 4.2883 | 45.44 | 0.1171 | 3 | 1.2958 | -0.2072 | -0.5479 | 1.4656 | 0.2799 | 1.5917 | -0.0246 | 0.0144 | 0.1746 | -0.113 | 0.1595 | -0.4448 | -0.485 | 0.6094 | -0.1348 | 0.2395 | -0.2939 | -0.0753 | 0.702 | -0.0835 | 0.3728 | 45.696 | 30.1186 | 2.1073 | 4 | 85.797 | -4.6945 | -1.9922 | 25.7471 | 5.9771 | 47.3141 | -0.5551 | -0.6975 | 0.1597 | 0.5878 | 0.7178 | -0.6563 | 0.5266 | 2.4069 | -0.1627 | -0.0134 | -0.0038 | 0.0147 | -0.0052 | -0.0056 | -0.0078 | 25.5072 | 4.1104 | 9.4729 | 5 | 14.7316 | -6.2487 | -34.4924 | 131.4311 | 60.4074 | 97.0321 | -0.7922 | -3.2011 | -1.3274 | -1.5039 | -2.1319 | 4.4994 | 1.7854 | 2.2815 | 2.9241 | -0.0096 | -0.022 | -0.0139 | -0.0581 | -0.0043 | -0.021 | -0.1383 | 32.0699 | 0.8638 | 6 | 130.9493 | 79.4837 | -65.2675 | 111.0212 | -78.3331 | 120.8683 | 1.1513 | 3.402 | 0.9457 | -1.8057 | -0.1297 | -0.6193 | -1.906 | 2.0445 | -1.0216 | 0.0052 | -0.0044 | 0.0035 | 0.0025 | -0.0077 | 0.0036 | 36.8593 | 39.1181 | -4.4406 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Selection: ALL ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | AA10 - 416 | 10 - 416 | 2 | 1 | AH1101 | | 3 | 1 | CD501 | | 4 | 2 | BB10 - 416 | 10 - 416 | 5 | 2 | BI1201 | | 6 | 2 | CD601 | | 7 | 3 | CC10 - 416 | 10 - 416 | 8 | 3 | CJ1301 | | 9 | 3 | CD701 | | 10 | 4 | AE801 | | 11 | 5 | BF901 | | 12 | 6 | CG1001 | | | | | | | | | | | | | | | | | | | | | | | | | |
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