ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | SERGUI | guiデータ収集 | | HKL-2000 | | データ削減 | | HKL-2000 | | データスケーリング | | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 2CMU 解像度: 2.1→30.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.84 / SU B: 9.861 / SU ML: 0.121 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.246 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.259 | 916 | 5.1 % | RANDOM |
---|
Rwork | 0.2 | - | - | - |
---|
obs | 0.202 | 18041 | 76.03 % | - |
---|
|
---|
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 |
---|
原子変位パラメータ | Biso max: 63.93 Å2 / Biso mean: 29.966 Å2 / Biso min: 8.97 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.85 Å2 | 0.42 Å2 | 0 Å2 |
---|
2- | - | 0.85 Å2 | 0 Å2 |
---|
3- | - | - | -1.27 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.1→30.37 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 2640 | 0 | 0 | 164 | 2804 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.02 | 0.022 | 2710 | X-RAY DIFFRACTION | r_angle_refined_deg1.853 | 1.967 | 3669 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.725 | 5 | 331 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg40.665 | 25.726 | 124 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.124 | 15 | 495 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.415 | 15 | 6 | X-RAY DIFFRACTION | r_chiral_restr0.13 | 0.2 | 413 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 2015 | X-RAY DIFFRACTION | r_nbd_refined0.215 | 0.2 | 1250 | X-RAY DIFFRACTION | r_nbtor_refined0.309 | 0.2 | 1820 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.186 | 0.2 | 198 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.227 | 0.2 | 33 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.218 | 0.2 | 6 | X-RAY DIFFRACTION | r_mcbond_it1.103 | 1.5 | 1707 | X-RAY DIFFRACTION | r_mcangle_it1.731 | 2 | 2674 | X-RAY DIFFRACTION | r_scbond_it2.869 | 3 | 1150 | X-RAY DIFFRACTION | r_scangle_it3.995 | 4.5 | 995 | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 2.1→2.156 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.262 | 50 | - |
---|
Rwork | 0.198 | 945 | - |
---|
all | - | 995 | - |
---|
obs | - | - | 57.71 % |
---|
|
---|
精密化 TLS | 手法: refined / Origin x: -8.5798 Å / Origin y: -0.6163 Å / Origin z: -17.9363 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | -0.0213 Å2 | 0.0472 Å2 | 0.0044 Å2 | - | -0.0602 Å2 | 0.006 Å2 | - | - | -0.0428 Å2 |
---|
L | 0.4165 °2 | -0.2493 °2 | 0.1388 °2 | - | 1.3127 °2 | 0.3324 °2 | - | - | 1.5693 °2 |
---|
S | 0.1205 Å ° | 0.0092 Å ° | -0.0191 Å ° | -0.1962 Å ° | -0.0355 Å ° | -0.0655 Å ° | -0.0619 Å ° | -0.1005 Å ° | -0.0851 Å ° |
---|
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | A1 - 330 | 2 | X-RAY DIFFRACTION | 1 | A333 - 494 | | |
|
---|