ソフトウェア | 名称 | バージョン | 分類 |
---|
Aimless | 0.5.12データスケーリング | PHENIX | | 精密化 | PDB_EXTRACT | 3.15 | データ抽出 | XDS | | データ削減 | Coot | | モデル構築 | |
|
---|
精密化 | 構造決定の手法: フーリエ合成 開始モデル: 2Q0I 解像度: 1.992→49.961 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 20.05 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.2056 | 1128 | 4.98 % |
---|
Rwork | 0.1621 | 21536 | - |
---|
obs | 0.1642 | 22664 | 99.97 % |
---|
|
---|
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 |
---|
原子変位パラメータ | Biso max: 140.57 Å2 / Biso mean: 45.7383 Å2 / Biso min: 21.47 Å2 |
---|
精密化ステップ | サイクル: final / 解像度: 1.992→49.961 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 2374 | 0 | 25 | 185 | 2584 |
---|
Biso mean | - | - | 33.92 | 46.79 | - |
---|
残基数 | - | - | - | - | 298 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.018 | 2493 | X-RAY DIFFRACTION | f_angle_d1.152 | 3379 | X-RAY DIFFRACTION | f_chiral_restr0.059 | 366 | X-RAY DIFFRACTION | f_plane_restr0.008 | 442 | X-RAY DIFFRACTION | f_dihedral_angle_d9.996 | 1482 | | | | | |
|
---|
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 % 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
---|
1.9921-2.0828 | 0.2649 | 149 | 0.2319 | 2619 | 2768 | 2.0828-2.1926 | 0.2674 | 141 | 0.2021 | 2646 | 2787 | 2.1926-2.33 | 0.2312 | 143 | 0.1788 | 2647 | 2790 | 2.33-2.5099 | 0.2156 | 127 | 0.1623 | 2649 | 2776 | 2.5099-2.7624 | 0.2313 | 139 | 0.1682 | 2681 | 2820 | 2.7624-3.1621 | 0.2182 | 147 | 0.1686 | 2677 | 2824 | 3.1621-3.9837 | 0.1735 | 136 | 0.1511 | 2743 | 2879 | 3.9837-49.9766 | 0.1906 | 146 | 0.148 | 2874 | 3020 |
|
---|
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) |
---|
1 | 3.0759 | -0.6093 | -0.6459 | 3.9155 | -1.2473 | 2.8416 | -0.0235 | 0.083 | -0.1019 | 0.1475 | 0.0993 | 0.2564 | -0.0832 | -0.274 | -0.0563 | 0.2652 | 0.0279 | 0.0258 | 0.2645 | -0.0043 | 0.2949 | -30.3902 | -10.7147 | -17.9739 | 2 | 2.0348 | -0.571 | 0.0371 | 4.2146 | -0.2462 | 1.6952 | 0.0005 | -0.0197 | -0.0894 | 0.4335 | 0.0474 | 0.4963 | -0.0816 | -0.3188 | -0.0502 | 0.3118 | 0.0453 | 0.0603 | 0.3524 | 0.0247 | 0.2918 | -33.1953 | -8.3555 | -13.2695 | 3 | 3.8053 | -0.076 | -0.6129 | 2.4285 | -0.4818 | 1.8359 | -0.165 | -1.0748 | -0.1629 | 0.9109 | 0.0881 | 0.1328 | 0.0322 | -0.2862 | 0.0624 | 0.6029 | 0.0372 | 0.1123 | 0.4901 | 0.0792 | 0.2817 | -29.7594 | -11.365 | -2.7808 | 4 | 4.0339 | 0.5733 | 2.3755 | 0.3558 | -0.9787 | 8.1264 | -0.3454 | -0.9776 | 0.9731 | 1.1989 | 0.2124 | 0.034 | -0.5526 | -0.4542 | 0.1706 | 0.7792 | 0.1803 | -0.0057 | 0.564 | -0.1896 | 0.4649 | -27.7337 | 3.7138 | -0.4292 | 5 | 4.1569 | 0.3462 | 0.2095 | 1.5837 | 0.8385 | 2.836 | -0.1641 | -0.8037 | 0.3244 | 0.4263 | 0.0989 | 0.2452 | -0.1214 | -0.5202 | 0.0271 | 0.5188 | 0.0788 | 0.0726 | 0.4324 | 0.0808 | 0.3054 | -31.5128 | -7.0722 | -4.1643 | 6 | 3.1678 | 0.5204 | -0.1555 | 1.4775 | 0.0034 | 1.6452 | -0.1172 | -0.031 | -0.3103 | 0.266 | 0.0996 | -0.1004 | 0.1767 | 0.0864 | 0.0126 | 0.333 | 0.0452 | -0.0389 | 0.2327 | -0.0069 | 0.2885 | -17.7381 | -14.5804 | -15.5793 | 7 | 1.7738 | 0.684 | -0.0438 | 2.9195 | -0.0678 | 2.5663 | -0.0707 | -0.2378 | -0.2032 | 0.6507 | -0.0261 | -0.5198 | 0.041 | 0.483 | 0.1284 | 0.3721 | 0.0559 | -0.126 | 0.3332 | 0.0121 | 0.3546 | -6.9119 | -7.2516 | -12.8682 | 8 | 3.1339 | -1.022 | -0.7519 | 4.1473 | 0.6105 | 1.9508 | 0.089 | 0.5067 | -0.0756 | -0.305 | -0.1519 | 0.0212 | 0.0437 | -0.0902 | 0.0832 | 0.3055 | 0.0371 | -0.0279 | 0.3008 | -0.0219 | 0.2837 | -14.8928 | -11.5294 | -24.9343 | 9 | 3.5273 | 4.1863 | -0.1529 | 6.4791 | 1.4801 | 2.4046 | -0.0639 | 0.1379 | -0.2276 | 0.2892 | 0.3761 | -0.5792 | -0.3801 | 0.4516 | -0.3338 | 0.361 | 0.0013 | -0.125 | 0.3492 | -0.0122 | 0.3654 | 0.1931 | 2.4727 | -17.0525 | 10 | 8.7893 | 2.5062 | 1.663 | 1.6994 | 1.0362 | 0.8209 | 0.0637 | 0.0841 | 1.702 | 0.0925 | -0.2339 | 0.4515 | -0.4859 | 0.008 | 0.1128 | 0.6623 | 0.0561 | -0.1189 | 0.3305 | -0.0062 | 0.6223 | -8.8809 | 12.4056 | -14.8906 | 11 | 8.7815 | 0.5967 | 2.5198 | 2.7847 | 0.663 | 4.5408 | -0.1205 | -1.0139 | 0.4127 | -0.0282 | 0.087 | 0.3466 | -0.3014 | -0.2366 | 0.0492 | 0.6281 | -0.0014 | -0.1137 | 0.3597 | -0.0752 | 0.4526 | -11.8902 | 6.8133 | -8.6585 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | (( chain 'A' and (resid 18 through 41 )) or ( chain 'S' and resid 6 ) or ( chain 'S' and resid 29 ) or ( chain 'S' and resid 46 ) or ( chain 'S' and resid 49 ) or ( chain 'S' and resid 51 ) or ( chain 'S' and resid 71 ) or ( chain 'S' and resid 75 ) or ( chain 'S' and resid 80 ) or ( chain 'S' and resid 87 ) or ( chain 'S' and resid 91 ) or ( chain 'S' and resid 112 ) or ( chain 'S' and resid 119 ) or ( chain 'S' and resid 131 ) or ( chain 'S' and resid 170 ))A18 - 41 | 2 | X-RAY DIFFRACTION | 1 | (( chain 'A' and (resid 18 through 41 )) or ( chain 'S' and resid 6 ) or ( chain 'S' and resid 29 ) or ( chain 'S' and resid 46 ) or ( chain 'S' and | | |
|
---|