ソフトウェア | 名称 | バージョン | 分類 |
---|
XDS | | データスケーリング | PHASER | | 位相決定 | REFMAC | 5.6.0117精密化 | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 3oca, native EhchA.01519.a 解像度: 1.7→41.936 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.581 / SU ML: 0.061 / Isotropic thermal model: isotropic, TLS / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.096 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.198 | 1062 | 5.1 % | RANDOM |
---|
Rwork | 0.17 | - | - | - |
---|
obs | 0.172 | 20709 | - | - |
---|
all | - | 20709 | - | - |
---|
|
---|
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 mean: 23.09 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.78 Å2 | 0 Å2 | 0.23 Å2 |
---|
2- | - | 1.67 Å2 | 0 Å2 |
---|
3- | - | - | -0.88 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.7→41.936 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 1329 | 0 | 30 | 183 | 1542 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.013 | 0.019 | 1404 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 946 | X-RAY DIFFRACTION | r_angle_refined_deg1.555 | 1.985 | 1905 | X-RAY DIFFRACTION | r_angle_other_deg0.941 | 3 | 2322 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.7 | 5 | 178 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.18 | 24.333 | 60 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.31 | 15 | 239 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.61 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 219 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 1562 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 276 | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it | | | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it | | | X-RAY DIFFRACTION | r_scbond_it | | | X-RAY DIFFRACTION | r_scangle_it | | | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 1.7→1.74 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.222 | 76 | - |
---|
Rwork | 0.199 | 1336 | - |
---|
obs | - | - | 94.26 % |
---|
|
---|
精密化 TLS | 手法: refined / Origin x: -9.261 Å / Origin y: 7.495 Å / Origin z: 16.014 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.0131 Å2 | -0.0125 Å2 | 0.0005 Å2 | - | 0.0846 Å2 | -0.0079 Å2 | - | - | 0.0449 Å2 |
---|
L | 0.9133 °2 | -0.2144 °2 | -0.3702 °2 | - | 0.5054 °2 | 0.4398 °2 | - | - | 3.4877 °2 |
---|
S | 0.0484 Å ° | 0.1776 Å ° | -0.0377 Å ° | -0.0005 Å ° | -0.0212 Å ° | 0.0466 Å ° | 0.0889 Å ° | -0.2702 Å ° | -0.0272 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 - 185 | 2 | X-RAY DIFFRACTION | 1 | A200 - 210 | 3 | X-RAY DIFFRACTION | 1 | A189 - 375 | | | |
|
---|