ソフトウェア | 名称 | バージョン | 分類 |
---|
PHENIX | (PHENIX.REFINE)精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | PHASER | | 位相決定 | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 2WQF 解像度: 1.895→60.402 Å / SU ML: 0.21 / σ(F): 2 / 位相誤差: 20.4 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.1971 | 855 | 5 % |
---|
Rwork | 0.1659 | - | - |
---|
obs | 0.1674 | 17078 | 93.9 % |
---|
|
---|
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 mean: 29.8 Å2 |
---|
精密化ステップ | サイクル: LAST / 解像度: 1.895→60.402 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 1477 | 0 | 41 | 219 | 1737 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.004 | 1570 | X-RAY DIFFRACTION | f_angle_d0.804 | 2138 | X-RAY DIFFRACTION | f_dihedral_angle_d14.748 | 575 | X-RAY DIFFRACTION | f_chiral_restr0.052 | 230 | X-RAY DIFFRACTION | f_plane_restr0.003 | 276 | | | | | |
|
---|
LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
1.8951-2.0138 | 0.3229 | 104 | 0.2829 | 1982 | X-RAY DIFFRACTION | 70 | 2.0138-2.1693 | 0.2454 | 142 | 0.2125 | 2683 | X-RAY DIFFRACTION | 94 | 2.1693-2.3876 | 0.2116 | 149 | 0.1706 | 2830 | X-RAY DIFFRACTION | 100 | 2.3876-2.7331 | 0.1733 | 151 | 0.1517 | 2869 | X-RAY DIFFRACTION | 100 | 2.7331-3.4434 | 0.1797 | 152 | 0.1467 | 2880 | X-RAY DIFFRACTION | 100 | 3.4434-60.4327 | 0.1789 | 157 | 0.1501 | 2979 | X-RAY DIFFRACTION | 99 |
|
---|
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 | 4.7913 | -0.1099 | -1.64 | 1.6587 | 1.9027 | 2.6449 | 0.0594 | -0.2572 | -0.1759 | 0.0125 | -0.0466 | 0.0043 | 0.013 | 0.2982 | 0.0319 | 0.1837 | 0.0489 | -0.0368 | 0.1691 | 0.0481 | 0.1722 | -15.3 | -29.7028 | 13.9601 | 2 | 3.4801 | -1.7829 | -2.19 | 4.8389 | -0.126 | 4.47 | -0.3094 | 0.6854 | -0.9404 | -0.4984 | -0.1446 | 0.2868 | 0.525 | 0.0856 | 0.1986 | 0.2337 | 0.009 | 0.0198 | 0.2287 | -0.0707 | 0.219 | -24.9787 | -29.049 | 2.3439 | 3 | 0.9932 | -0.9907 | 0.3349 | 2.4008 | -0.651 | 1.8778 | -0.0263 | 0.3177 | 0.3801 | -0.1816 | -0.1076 | -0.4804 | -0.1745 | 0.3474 | -0.0574 | 0.2369 | -0.0514 | -0.0078 | 0.2142 | 0.0068 | 0.2642 | -14.6579 | -14.6293 | 3.0984 | 4 | 3.869 | -0.2893 | -1.13 | 1.2597 | 0.2607 | 3.0872 | -0.1456 | 0.395 | 0.4501 | 0.0824 | 0.0172 | 0.115 | -0.3958 | -0.5158 | 0.0999 | 0.2694 | 0.0416 | -0.0401 | 0.1576 | 0.0371 | 0.2548 | -31.5051 | -8.8044 | 5.6288 | 5 | 4.61 | -3.5442 | -0.3864 | 6.303 | 0.0333 | 2.8033 | -0.0575 | -0.3169 | 0.158 | -0.093 | 0.1651 | 0.2676 | -0.4426 | -0.1746 | -0.0735 | 0.1829 | 0.0054 | -0.0198 | 0.1304 | -0.0176 | 0.1814 | -28.786 | -16.0145 | 13.7388 | 6 | 2.1043 | -1.3286 | 0.0803 | 3.6051 | -0.9335 | 2.5222 | 0.084 | 0.2366 | 0.3626 | -0.2172 | -0.1396 | -0.2404 | -0.3328 | 0.1429 | 0.0739 | 0.2416 | -0.0337 | 0.0107 | 0.2367 | 0.0325 | 0.2733 | -17.369 | -12.2066 | 3.5162 | 7 | 1.9746 | -0.617 | -1.7735 | 1.0421 | 1.2305 | 5.539 | -0.0911 | -0.486 | -0.0058 | 0.1969 | 0.1446 | -0.1126 | 0.1402 | 0.4846 | -0.0289 | 0.2073 | 0.0097 | -0.0312 | 0.1972 | 0.0195 | 0.2046 | -17.3834 | -23.3328 | 28.8986 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | CHAIN A AND (RESID 2 THROUGH 22 )2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 23 THROUGH 35 )3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 36 THROUGH 96 )4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESID 97 THROUGH 115 )5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESID 116 THROUGH 144 )6 | X-RAY DIFFRACTION | 6 | CHAIN A AND (RESID 145 THROUGH 180 )7 | X-RAY DIFFRACTION | 7 | CHAIN A AND (RESID 181 THROUGH 202 ) | | | | | | |
|
---|