ソフトウェア | 名称 | バージョン | 分類 |
---|
ADSC | Quantumデータ収集 | AMoRE | | 位相決定 | CNS | 1.2 | 精密化 | DPS | | データ削減 | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 355D 解像度: 2.7→9.86 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 229102.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.281 | 189 | 9.4 % | RANDOM |
---|
Rwork | 0.212 | - | - | - |
---|
obs | 0.212 | 2021 | 100 % | - |
---|
|
---|
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 29.1181 Å2 / ksol: 0.35 e/Å3 |
---|
原子変位パラメータ | Biso mean: 42.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 12.68 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | -1.03 Å2 | 0 Å2 |
---|
3- | - | - | -11.65 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.48 Å | 0.36 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.58 Å | 0.45 Å |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.7→9.86 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 0 | 490 | 22 | 45 | 557 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal |
---|
X-RAY DIFFRACTION | c_bond_d0.007 | 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 | X-RAY DIFFRACTION | c_angle_deg_na | X-RAY DIFFRACTION | c_angle_deg_prot | X-RAY DIFFRACTION | c_dihedral_angle_d16.5 | X-RAY DIFFRACTION | c_dihedral_angle_d_na | X-RAY DIFFRACTION | c_dihedral_angle_d_prot | X-RAY DIFFRACTION | c_improper_angle_d1.23 | X-RAY DIFFRACTION | c_improper_angle_d_na | X-RAY DIFFRACTION | c_improper_angle_d_prot | X-RAY DIFFRACTION | c_mcbond_it | X-RAY DIFFRACTION | c_mcangle_it | X-RAY DIFFRACTION | c_scbond_it | X-RAY DIFFRACTION | c_scangle_it | | | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 2.7→2.87 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 6
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.469 | 37 | 11.6 % |
---|
Rwork | 0.39 | 283 | - |
---|
obs | - | - | 100 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 2 | water_rep.paramwater.topX-RAY DIFFRACTION | 3 | formylu.paramformylu.topX-RAY DIFFRACTION | 4 | dapi.paramdapi.topX-RAY DIFFRACTION | 5 | noNH.paramnoNH.top | | | | | | | |
|
---|