ソフトウェア | 名称 | バージョン | 分類 |
---|
REFMAC | 5.8.0267精密化 | CrysalisPro | | データ削減 | Aimless | | 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: 2ZAL 解像度: 2.55→20.358 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.841 / SU ML: 0.268 / 交差検証法: FREE R-VALUE / ESU R: 2.323 / ESU R Free: 0.33
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.2483 | 1010 | 5.632 % |
---|
Rwork | 0.2023 | 16922 | - |
---|
all | 0.205 | - | - |
---|
obs | - | 17932 | 92.044 % |
---|
|
---|
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 BULK SOLVENT |
---|
原子変位パラメータ | Biso mean: 33.407 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.204 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 1.543 Å2 | -0 Å2 |
---|
3- | - | - | -1.747 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.55→20.358 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 4022 | 0 | 2 | 142 | 4166 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.009 | 0.013 | 4091 | X-RAY DIFFRACTION | r_bond_other_d0.007 | 0.015 | 3906 | X-RAY DIFFRACTION | r_angle_refined_deg1.585 | 1.629 | 5551 | X-RAY DIFFRACTION | r_angle_other_deg1.39 | 1.57 | 8968 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.093 | 5 | 554 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg30.155 | 22.581 | 186 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.067 | 15 | 639 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.894 | 15 | 24 | X-RAY DIFFRACTION | r_chiral_restr0.065 | 0.2 | 547 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 4754 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 878 | X-RAY DIFFRACTION | r_nbd_refined0.205 | 0.2 | 902 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.197 | 0.2 | 3954 | X-RAY DIFFRACTION | r_nbtor_refined0.157 | 0.2 | 1969 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.08 | 0.2 | 1913 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.152 | 0.2 | 138 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.044 | 0.2 | 2 | X-RAY DIFFRACTION | r_metal_ion_refined0.187 | 0.2 | 5 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.325 | 0.2 | 20 | X-RAY DIFFRACTION | r_nbd_other0.326 | 0.2 | 48 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.399 | 0.2 | 2 | X-RAY DIFFRACTION | r_mcbond_it1.468 | 2.364 | 2219 | X-RAY DIFFRACTION | r_mcbond_other1.467 | 2.362 | 2218 | X-RAY DIFFRACTION | r_mcangle_it2.611 | 3.536 | 2766 | X-RAY DIFFRACTION | r_mcangle_other2.61 | 3.538 | 2767 | X-RAY DIFFRACTION | r_scbond_it1.365 | 2.643 | 1872 | X-RAY DIFFRACTION | r_scbond_other1.363 | 2.64 | 1870 | X-RAY DIFFRACTION | r_scangle_it2.374 | 3.866 | 2783 | X-RAY DIFFRACTION | r_scangle_other2.373 | 3.866 | 2783 | X-RAY DIFFRACTION | r_lrange_it5.949 | 43.913 | 16300 | X-RAY DIFFRACTION | r_lrange_other5.925 | 43.944 | 16259 | X-RAY DIFFRACTION | r_ncsr_local_group_10.133 | 0.05 | 3932 | X-RAY DIFFRACTION | r_ncsr_local_group_20.126 | 0.05 | 3526 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Refine-ID | タイプ | Rms dev position (Å) | Weight position |
---|
1 | 1 | AAAX-RAY DIFFRACTION | Local ncs0.13294 | 0.05007 | 1 | 2 | CCCX-RAY DIFFRACTION | Local ncs0.13294 | 0.05007 | 2 | 3 | BBBX-RAY DIFFRACTION | Local ncs0.12641 | 0.05007 | 2 | 4 | DDDX-RAY DIFFRACTION | Local ncs0.12641 | 0.05007 | | | | | | | | |
|
---|
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 (%) |
---|
2.55-2.615 | 0.351 | 75 | 0.319 | 1239 | X-RAY DIFFRACTION | 94.7368 | 2.615-2.686 | 0.277 | 70 | 0.291 | 1239 | X-RAY DIFFRACTION | 95.2 | 2.686-2.762 | 0.355 | 50 | 0.284 | 1186 | X-RAY DIFFRACTION | 94.3511 | 2.762-2.845 | 0.43 | 59 | 0.273 | 1139 | X-RAY DIFFRACTION | 92.9403 | 2.845-2.937 | 0.31 | 58 | 0.258 | 1113 | X-RAY DIFFRACTION | 94.0562 | 2.937-3.038 | 0.311 | 68 | 0.253 | 1060 | X-RAY DIFFRACTION | 92.7632 | 3.038-3.15 | 0.273 | 68 | 0.231 | 1015 | X-RAY DIFFRACTION | 93.2014 | 3.15-3.275 | 0.283 | 62 | 0.218 | 978 | X-RAY DIFFRACTION | 91.954 | 3.275-3.417 | 0.243 | 67 | 0.209 | 918 | X-RAY DIFFRACTION | 90.0366 | 3.417-3.578 | 0.264 | 52 | 0.189 | 911 | X-RAY DIFFRACTION | 93.2236 | 3.578-3.765 | 0.259 | 49 | 0.222 | 821 | X-RAY DIFFRACTION | 87.0871 | 3.765-3.985 | 0.244 | 60 | 0.179 | 810 | X-RAY DIFFRACTION | 90.8142 | 3.985-4.249 | 0.204 | 47 | 0.149 | 761 | X-RAY DIFFRACTION | 91.61 | 4.249-4.573 | 0.148 | 44 | 0.127 | 712 | X-RAY DIFFRACTION | 90 | 4.573-4.984 | 0.157 | 39 | 0.131 | 676 | X-RAY DIFFRACTION | 91.0828 | 4.984-5.531 | 0.22 | 51 | 0.151 | 600 | X-RAY DIFFRACTION | 90.795 | 5.531-6.31 | 0.207 | 35 | 0.174 | 567 | X-RAY DIFFRACTION | 92.4731 | 6.31-7.549 | 0.244 | 22 | 0.158 | 499 | X-RAY DIFFRACTION | 91.2434 | 7.549-10.01 | 0.192 | 18 | 0.131 | 392 | X-RAY DIFFRACTION | 89.9123 | 10.01-20.358 | 0.21 | 16 | 0.212 | 286 | X-RAY DIFFRACTION | 92.9231 |
|
---|
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 | 0.6493 | -0.3369 | -0.346 | 0.4862 | -0.2436 | 0.9241 | 0.03 | 0.0494 | 0.1526 | -0.064 | 0.028 | -0.0133 | 0.1304 | -0.0617 | -0.058 | 0.0478 | 0.0044 | 0.0466 | 0.1515 | 0.043 | 0.1354 | 4.4 | 7.62 | 27.961 | 2 | 0.4083 | -0.1925 | 0.1931 | 0.7424 | -0.4947 | 0.8887 | 0.0382 | -0.079 | 0.0803 | -0.0797 | -0.1379 | -0.0454 | 0.1969 | 0.1531 | 0.0997 | 0.0468 | 0.033 | 0.026 | 0.1751 | 0.0288 | 0.0373 | 16.953 | -0.166 | 31.206 | 3 | 0.7725 | 0.4208 | 0.5289 | 0.3903 | 0.1483 | 1.4806 | -0.1892 | -0.0973 | -0.0101 | -0.0447 | -0.0111 | 0.051 | -0.0135 | -0.0613 | 0.2003 | 0.1003 | 0.0734 | 0.059 | 0.1509 | -0.0035 | 0.1014 | 3.373 | -5.65 | 61.099 | 4 | 0.777 | 0.1321 | -0.0103 | 0.0797 | 0.1847 | 0.8989 | -0.2174 | -0.0058 | 0.0113 | -0.0387 | 0.0236 | 0.0459 | -0.0689 | 0.2323 | 0.1938 | 0.0928 | 0.0144 | -0.0306 | 0.2198 | 0.0081 | 0.0584 | 17.381 | -0.195 | 57.634 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | ALLAAA2 - 145 | 2 | X-RAY DIFFRACTION | 2 | ALLBBB179 - 313 | 3 | X-RAY DIFFRACTION | 3 | ALLCCC4 - 145 | 4 | X-RAY DIFFRACTION | 4 | ALLDDD179 - 313 | | | | | | | | |
|
---|