ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
XSCALE | | データスケーリング | | MOLREP | | 位相決定 | | REFMAC | 5.2.0003精密化 | | PDB_EXTRACT | 3 | データ抽出 | | XDS | | データ削減 | | |
|
---|
精密化 | 構造決定の手法: 分子置換 / 解像度: 2.6→20 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.767 / SU B: 26.351 / SU ML: 0.537 / TLS residual ADP flag: UNVERIFIED / 交差検証法: THROUGHOUT / ESU R: 0.85 / ESU R Free: 0.432 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Twinning operator is h,-k,-l. Twinning perfect pseudo-merohedral twin.
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.35867 | 1158 | 5.2 % | RANDOM |
---|
Rwork | 0.29563 | - | - | - |
---|
obs | 0.29889 | 21123 | 98.92 % | - |
---|
|
---|
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: BABINET MODEL WITH MASK |
---|
原子変位パラメータ | Biso mean: 31.398 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -2.01 Å2 | 0 Å2 | -0.46 Å2 |
---|
2- | - | -1.28 Å2 | 0 Å2 |
---|
3- | - | - | 3.29 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.6→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 4352 | 0 | 0 | 0 | 4352 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.009 | 0.022 | 4436 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.301 | 1.952 | 6022 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.983 | 5 | 574 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg43.813 | 26.105 | 190 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg18.346 | 15 | 740 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.698 | 15 | 12 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 678 | X-RAY DIFFRACTION | r_gen_planes_refined0.002 | 0.02 | 3354 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.201 | 0.2 | 1209 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.292 | 0.2 | 2883 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.117 | 0.2 | 52 | 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_refined0.071 | 0.2 | 2 | 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_it0.173 | 1.5 | 2935 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.311 | 2 | 4550 | X-RAY DIFFRACTION | r_scbond_it0.307 | 3 | 1738 | X-RAY DIFFRACTION | r_scangle_it0.487 | 4.5 | 1472 | 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: 2.6→2.668 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.27 | 76 | - |
---|
Rwork | 0.261 | 1580 | - |
---|
obs | - | - | 98.98 % |
---|
|
---|
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 | 1.4407 | 0.0902 | -0.1617 | 1.4411 | -0.2315 | 1.0859 | 0.0311 | -0.0608 | -0.3351 | 0.1418 | -0.0132 | -0.053 | 0.102 | 0.0209 | -0.0179 | -0.0404 | -0.0256 | -0.0128 | -0.036 | 0.0363 | -0.0257 | 16.251 | -9.022 | 16.07 | 2 | 0.9136 | 0.2561 | 0.2198 | 1.8065 | -0.5289 | 1.459 | -0.0177 | 0.0289 | 0.0783 | -0.089 | 0.0211 | -0.005 | -0.1916 | -0.0798 | -0.0033 | -0.0336 | -0.0136 | 0.0124 | 0.0114 | 0.0153 | -0.0862 | 15.272 | 14.485 | 0.559 | 3 | 0.7759 | 0.4424 | 0.5718 | 2.2822 | 0.3544 | 3.0136 | -0.2335 | 0.0716 | 0.2677 | -0.2776 | -0.095 | 0.0979 | -0.5017 | 0.0636 | 0.3285 | -0.0093 | -0.0005 | -0.0646 | -0.0831 | 0.0042 | -0.0342 | 2.332 | -37.267 | 4.912 | 4 | 1.5806 | -0.42 | -0.0191 | 2.2816 | -0.3633 | 2.0747 | -0.0768 | -0.0617 | -0.1297 | 0.0794 | -0.0681 | 0.0659 | 0.2335 | -0.1025 | 0.1449 | -0.0743 | -0.0082 | 0.0336 | -0.0528 | -0.0339 | -0.0847 | 0.255 | -60.891 | 20.398 |
|
---|
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 | AA31 - 114 | 4 - 87 | 2 | X-RAY DIFFRACTION | 1 | AA235 - 314 | 208 - 287 | 3 | X-RAY DIFFRACTION | 2 | AA120 - 230 | 93 - 203 | 4 | X-RAY DIFFRACTION | 3 | BB31 - 114 | 4 - 87 | 5 | X-RAY DIFFRACTION | 3 | BB235 - 314 | 208 - 287 | 6 | X-RAY DIFFRACTION | 4 | BB120 - 230 | 93 - 203 | | | | | | | | | | | | |
|
---|