ソフトウェア | 名称 | バージョン | 分類 |
---|
AMoRE | | 位相決定 | CNS | 1 | 精密化 | DENZO | | データ削減 | SCALEPACK | | 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: 1K26, same protein solved by SAD with iridium derivative data. 解像度: 1.8→19.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1466528.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.22 | 2463 | 8.1 % | RANDOM |
---|
Rwork | 0.184 | - | - | - |
---|
all | - | 30585 | - | - |
---|
obs | - | 30585 | 98.7 % | - |
---|
|
---|
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 46.1588 Å2 / ksol: 0.38221 e/Å3 |
---|
原子変位パラメータ | Biso mean: 21.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -3.46 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | -0.32 Å2 | 0 Å2 |
---|
3- | - | - | 3.79 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.23 Å | 0.18 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.17 Å | 0.13 Å |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.8→19.74 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 2414 | 0 | 56 | 243 | 2713 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.016 | | X-RAY DIFFRACTION | c_bond_d_na | | X-RAY DIFFRACTION | c_bond_d_prot | | X-RAY DIFFRACTION | c_angle_d | | X-RAY DIFFRACTION | c_angle_d_na | | X-RAY DIFFRACTION | c_angle_d_prot | | X-RAY DIFFRACTION | c_angle_deg1.7 | | X-RAY DIFFRACTION | c_angle_deg_na | | X-RAY DIFFRACTION | c_angle_deg_prot | | X-RAY DIFFRACTION | c_dihedral_angle_d24.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d_na | | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | | X-RAY DIFFRACTION | c_improper_angle_d1.09 | | X-RAY DIFFRACTION | c_improper_angle_d_na | | X-RAY DIFFRACTION | c_improper_angle_d_prot | | X-RAY DIFFRACTION | c_mcbond_it1.84 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.56 | 2 | X-RAY DIFFRACTION | c_scbond_it3.14 | 2 | X-RAY DIFFRACTION | c_scangle_it4.48 | 2.5 | | | | | | | | | | | | | | | | | | | |
|
---|
Refine LS restraints NCS | NCS model details: CONSTRAINED |
---|
LS精密化 シェル | 解像度: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.289 | 393 | 8.1 % |
---|
Rwork | 0.234 | 4457 | - |
---|
obs | - | 4838 | 95.6 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMWATER_REP.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.TOPX-RAY DIFFRACTION | 4 | OTHERS.PAROTHERS.TOP | | | | | | | |
|
---|
精密化 | *PLUS 最高解像度: 1.8 Å / 最低解像度: 20 Å / % reflection Rfree: 8 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.183 |
---|
溶媒の処理 | *PLUS |
---|
原子変位パラメータ | *PLUS |
---|
拘束条件 | *PLUS Refine-ID | タイプ | Dev ideal |
---|
X-RAY DIFFRACTION | c_bond_d0.019 | X-RAY DIFFRACTION | c_angle_deg1.8 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg24.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.09 | | | | | | |
|
---|
LS精密化 シェル | *PLUS Rfactor Rfree: 0.289 / Rfactor Rwork: 0.234 |
---|