ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
PHENIX | 1.8_1069精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | XDS | | データスケーリング | | XDS | | データ削減 | | 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 3LA5 解像度: 2.15→47.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.34 / 位相誤差: 35.69 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.2548 | 523 | 4.8 % |
---|
Rwork | 0.2038 | - | - |
---|
obs | 0.2064 | 10894 | 99.33 % |
---|
|
---|
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: 57.4802 Å2 |
---|
Refine analyze | Luzzati coordinate error obs: 0.34 Å |
---|
精密化ステップ | サイクル: LAST / 解像度: 2.15→47.5 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 0 | 1502 | 17 | 22 | 1541 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.005 | 1690 | X-RAY DIFFRACTION | f_angle_d0.91 | 2626 | X-RAY DIFFRACTION | f_dihedral_angle_d12.416 | 849 | X-RAY DIFFRACTION | f_chiral_restr0.038 | 355 | X-RAY DIFFRACTION | f_plane_restr0.007 | 72 | | | | | |
|
---|
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 (%) |
---|
2.15-2.3664 | 0.3853 | 113 | 0.2845 | 2525 | X-RAY DIFFRACTION | 100 | 2.3664-2.7088 | 0.3698 | 144 | 0.2943 | 2569 | X-RAY DIFFRACTION | 100 | 2.7088-3.4126 | 0.2495 | 113 | 0.2255 | 2577 | X-RAY DIFFRACTION | 99 | 3.4126-47.5841 | 0.2294 | 153 | 0.1712 | 2700 | X-RAY DIFFRACTION | 98 |
|
---|
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 | 5.376 | 5.0681 | -0.6838 | 4.785 | -0.6454 | 1.5892 | 1.5481 | 0.9021 | -0.0242 | -0.3869 | -0.7571 | 0.0073 | -0.0979 | -0.0727 | -0.8913 | 0.6712 | 0.0598 | -0.1411 | 0.6594 | 0.019 | 2.0568 | 40.9868 | 2.2936 | 10.9049 | 2 | 1.6643 | 1.1942 | 0.0783 | 1.0979 | 0.9459 | 3.1883 | 0.6525 | -2.4014 | -2.8153 | 0.7216 | -0.1337 | -0.6586 | 0.5467 | -0.2246 | -0.4457 | 0.4328 | -0.1065 | -0.1175 | 0.7603 | 0.3105 | 0.8811 | 28.4202 | 13.6993 | 21.4627 | 3 | 1.4555 | -1.3007 | 0.1929 | 3.3839 | -1.3924 | 1.4851 | 0.2177 | 0.3997 | -0.1498 | -0.3348 | -0.0109 | 0.7568 | -0.1003 | 0.137 | -0.183 | 0.2997 | 0.0179 | -0.0508 | 0.3316 | -0.0779 | 0.4148 | 14.1389 | 31.2092 | 7.1471 | 4 | 6.6237 | 0.4157 | 1.8766 | 4.7295 | 1.1631 | 3.1 | 0.0957 | 0.2678 | -0.8787 | -0.3078 | 0.1551 | 0.3965 | 0.1585 | 0.303 | -0.2897 | 0.3239 | -0.0236 | -0.0128 | 0.2878 | 0.0174 | 0.3293 | 22.2728 | 19.3067 | 10.5227 | 5 | 2.2903 | 0.984 | 0.2502 | 0.6643 | 0.858 | 2.0528 | 0.3342 | -0.3762 | -1.3576 | -0.2421 | -0.1411 | 2.1342 | -0.134 | -0.537 | -0.2198 | 0.3817 | 0.0642 | -0.1401 | 0.4433 | 0.0853 | 1.0893 | 4.2042 | 22.9059 | 8.6218 | 6 | 0.5077 | -1.8255 | -0.375 | 6.7337 | 0.8123 | 2.0067 | 0.2365 | -0.2628 | -2.3146 | 0.3085 | 0.0031 | -0.8283 | 0.2693 | -0.3174 | -0.2233 | 0.3598 | -0.0375 | -0.1297 | 0.5894 | 0.0197 | 1.3144 | 38.1733 | 6.6274 | 16.1388 |
|
---|
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 13 through 18 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 19 through 24 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 25 through 46 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 47 through 61 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 62 through 72 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 73 through 83 ) | | | | | |
|
---|