ソフトウェア | 名称 | バージョン | 分類 |
---|
REFMAC | 5.2.0019精密化 | SBC-Collect | | データ収集 | HKL-2000 | | データスケーリング | HKL-3000 | | 位相決定 | SHELXE | | モデル構築 | SOLVE | | 位相決定 | RESOLVE | | 位相決定 | ARP/wARP | | モデル構築 | |
|
---|
精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.9→47.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.984 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / 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 | 0.22054 | 919 | 5.1 % | RANDOM |
---|
Rwork | 0.17771 | - | - | - |
---|
all | 0.17988 | 17063 | - | - |
---|
obs | 0.17988 | 17063 | 99.66 % | - |
---|
|
---|
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: 18.295 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.36 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 0.52 Å2 | 0 Å2 |
---|
3- | - | - | -0.88 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.9→47.51 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 1595 | 0 | 31 | 216 | 1842 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.017 | 0.022 | 1660 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.422 | 1.97 | 2240 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.707 | 5 | 194 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.203 | 24.375 | 80 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.665 | 15 | 303 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg10.819 | 15 | 10 | X-RAY DIFFRACTION | r_chiral_restr0.098 | 0.2 | 236 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 1236 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.214 | 0.2 | 781 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.307 | 0.2 | 1158 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.183 | 0.2 | 179 | 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_refined0.187 | 0.2 | 82 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.254 | 0.2 | 26 | 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_it1.468 | 1.5 | 1012 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.541 | 2 | 1566 | X-RAY DIFFRACTION | r_scbond_it3.026 | 3 | 799 | X-RAY DIFFRACTION | r_scangle_it4.338 | 4.5 | 674 | 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: 1.9→1.949 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.246 | 66 | - |
---|
Rwork | 0.159 | 1233 | - |
---|
obs | - | - | 99.92 % |
---|
|
---|
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 | 2.9091 | -0.1366 | -0.5306 | 1.0702 | 0.2535 | 1.4882 | -0.0421 | -0.1879 | -0.1786 | 0.1582 | 0.047 | -0.0417 | 0.1616 | 0.1513 | -0.0049 | -0.0574 | 0.0119 | -0.0191 | -0.062 | 0.0207 | -0.074 | 4.573 | 6.73 | 35.565 | 2 | 0.1854 | -0.0476 | -0.161 | 0.1044 | -0.0197 | 0.571 | 0.0874 | 0.0459 | -0.0655 | -0.0255 | 0.0015 | -0.101 | -0.049 | 0.1606 | -0.0888 | 0.0354 | -0.0017 | 0.0184 | 0.0375 | -0.0107 | 0.0544 | 8.262 | 15.941 | 15.475 | 3 | 1.5594 | -0.364 | -0.0256 | 1.6856 | 2.1484 | 4.1775 | 0.0992 | 0.1582 | 0.1021 | -0.0846 | -0.0169 | 0.2364 | -0.3518 | -0.5945 | -0.0822 | 0.0605 | 0.097 | 0.0096 | 0.0148 | 0.0889 | -0.0266 | -12.748 | 27.07 | 10.063 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | AA2 - 18 | 2 - 18 | 2 | X-RAY DIFFRACTION | 1 | AA199 - 216 | 199 - 216 | 3 | X-RAY DIFFRACTION | 2 | AA19 - 87 | 19 - 87 | 4 | X-RAY DIFFRACTION | 2 | AA131 - 198 | 131 - 198 | 5 | X-RAY DIFFRACTION | 3 | AA88 - 130 | 88 - 130 | | | | | | | | | | |
|
---|