ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | HKL-2000 | | データスケーリング | PHENIX | (phenix.refine: 1.9_1682)精密化 | PDB_EXTRACT | 3.15 | データ抽出 | PHENIX | | 位相決定 | |
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精密化 | 解像度: 2.49→31.958 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.59 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2249 | 1556 | 5.04 % |
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Rwork | 0.1722 | 29346 | - |
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obs | 0.1749 | 30902 | 99.25 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 128.38 Å2 / Biso mean: 41.3601 Å2 / Biso min: 12.23 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.49→31.958 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6481 | 0 | 0 | 328 | 6809 |
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Biso mean | - | - | - | 32.63 | - |
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残基数 | - | - | - | - | 881 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.004 | 6587 | X-RAY DIFFRACTION | f_angle_d0.791 | 8900 | X-RAY DIFFRACTION | f_chiral_restr0.031 | 1028 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1165 | X-RAY DIFFRACTION | f_dihedral_angle_d12.569 | 2422 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A4940 | X-RAY DIFFRACTION | 14.376 | TORSIONAL1 | 2 | B4940 | X-RAY DIFFRACTION | 14.376 | TORSIONAL | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.49-2.5708 | 0.2905 | 114 | 0.234 | 2564 | 2678 | 96 | 2.5708-2.6626 | 0.3049 | 135 | 0.24 | 2635 | 2770 | 99 | 2.6626-2.7692 | 0.2828 | 140 | 0.2319 | 2617 | 2757 | 99 | 2.7692-2.8952 | 0.2468 | 134 | 0.2101 | 2645 | 2779 | 100 | 2.8952-3.0477 | 0.2892 | 142 | 0.1967 | 2652 | 2794 | 100 | 3.0477-3.2385 | 0.2553 | 143 | 0.1999 | 2659 | 2802 | 100 | 3.2385-3.4882 | 0.2647 | 154 | 0.1913 | 2653 | 2807 | 100 | 3.4882-3.8387 | 0.2199 | 130 | 0.1604 | 2681 | 2811 | 100 | 3.8387-4.393 | 0.1716 | 161 | 0.133 | 2698 | 2859 | 100 | 4.393-5.53 | 0.1834 | 142 | 0.1329 | 2720 | 2862 | 100 | 5.53-31.9609 | 0.1835 | 161 | 0.1409 | 2822 | 2983 | 99 |
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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 | 2.2244 | 1.8363 | 1.2111 | 1.7157 | 0.6692 | 1.3825 | -0.1077 | 0.2489 | -0.1864 | -0.0013 | 0.1749 | -0.2665 | -0.0175 | 0.3663 | -0.0019 | 0.2485 | 0.0046 | 0.0318 | 0.2441 | 0.0251 | 0.2029 | 2.2755 | 35.0783 | -18.9194 | 2 | 2.0815 | 0.0831 | -0.2611 | 2.1176 | 0.1524 | 2.3824 | 0.0275 | -0.1677 | -0.0002 | 0.1497 | -0.0396 | -0.0041 | 0.1002 | 0.2103 | 0.0295 | 0.198 | -0.0108 | -0.0062 | 0.2165 | 0.0029 | 0.1885 | -2.4095 | 10.4668 | -24.0992 | 3 | 0.4814 | 1.2514 | 0.413 | 3.0987 | 1.1537 | 1.2274 | 0.0401 | -0.1079 | 0.0551 | 0.2527 | -0.1872 | 0.373 | -0.0393 | -0.0916 | 0.156 | 0.2234 | 0.0321 | 0.0464 | 0.2613 | -0.0294 | 0.2794 | -9.1989 | 29.2692 | -12.6321 | 4 | 3.0135 | -0.2305 | 1.0424 | 2.5333 | 0.6167 | 2.6701 | 0.0143 | 0.041 | -0.1505 | 0.2886 | 0.0706 | -0.0381 | 0.1936 | 0.1651 | -0.084 | 0.2716 | 0.0298 | 0.0024 | 0.2201 | -0.0229 | 0.2187 | 6.4809 | 35.988 | -5.852 | 5 | 1.3385 | -0.097 | -0.1898 | 2.5648 | -1.5424 | 1.9849 | 0.0528 | -0.1977 | 0.0616 | 0.4591 | -0.0017 | 0.1543 | -0.4142 | -0.1699 | -0.0742 | 0.321 | -0.0052 | -0.0617 | 0.2864 | 0.0256 | 0.2601 | 37.0809 | 26.9704 | -38.6212 | 6 | 3.0919 | 0.9196 | -0.6308 | 1.3117 | -0.2087 | 1.4932 | -0.0747 | -0.3122 | -0.4787 | 0.0122 | -0.0483 | -0.1475 | 0.0448 | 0.0444 | 0.0923 | 0.233 | 0.0165 | 0.0024 | 0.2607 | 0.0841 | 0.3351 | 29.0092 | 2.5811 | -32.7616 | 7 | 1.4664 | 0.6716 | -1.0461 | 3.8922 | -1.3847 | 1.4104 | 0.0058 | -0.1034 | -0.2956 | -0.2079 | -0.2348 | -0.3279 | 0.0054 | 0.0958 | 0.2473 | 0.2069 | 0.0135 | -0.0236 | 0.3102 | 0.0312 | 0.2767 | 44.3636 | 16.3823 | -44.2279 | 8 | 2.6239 | -1.6075 | 0.4443 | 2.9881 | -1.1143 | 2.8913 | 0.2449 | 0.3457 | -0.1927 | -0.3546 | -0.1089 | 0.4514 | -0.2573 | -0.5374 | -0.1075 | 0.3647 | 0.0658 | -0.0624 | 0.382 | -0.0086 | 0.3638 | 34.398 | 29.9399 | -51.9689 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND RESID 312:345 )A312 - 345 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 346:517 )A346 - 517 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 518:594 )A518 - 594 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 595:756 )A595 - 756 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN B AND RESID 313:344 )B313 - 344 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN B AND RESID 345:517 )B345 - 517 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN B AND RESID 518:594 )B518 - 594 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN B AND RESID 595:756 )B595 - 756 | | | | | | | | | | | | | | | | |
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