ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
CNS | 1.1 | 精密化 | | DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | CNS | | 位相決定 | |
|
---|
精密化 | 構造決定の手法: Difference fourier / 解像度: 2.8→34.92 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.281 | 2008 | 9.8 % | random |
---|
Rwork | 0.227 | - | - | - |
---|
all | 0.238 | 21507 | - | - |
---|
obs | 0.238 | 20416 | 94.9 % | - |
---|
|
---|
溶媒の処理 | 溶媒モデル: CNS bulk solvent model used / Bsol: 23.3335 Å2 / ksol: 0.310044 e/Å3 |
---|
原子変位パラメータ | Biso max: 83.78 Å2 / Biso mean: 49.83 Å2 / Biso min: 19.46 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 3.88 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 3.88 Å2 | 0 Å2 |
---|
3- | - | - | -7.75 Å2 |
---|
|
---|
Refine Biso | クラス | Refine-ID | Treatment |
---|
polymerX-RAY DIFFRACTION | isotropicwaterX-RAY DIFFRACTION | isotropicnonpolymerX-RAY DIFFRACTION | isotropic | | | | | |
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.44 Å | 0.36 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.57 Å | 0.51 Å |
---|
Luzzati d res high | - | 2.8 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.8→34.92 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 4063 | 0 | 78 | 32 | 4173 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | x_bond_d0.008 | | X-RAY DIFFRACTION | x_angle_deg1.4 | | X-RAY DIFFRACTION | x_torsion_deg23.7 | | X-RAY DIFFRACTION | x_torsion_impr_deg0.98 | | X-RAY DIFFRACTION | x_mcbond_it1.04 | 1.5 | X-RAY DIFFRACTION | x_mcangle_it1.82 | 2 | X-RAY DIFFRACTION | x_scbond_it1.49 | 2 | X-RAY DIFFRACTION | x_scangle_it2.36 | 2.5 | | | | | | | | |
|
---|
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | % reflection Rfree (%) | Rfactor Rwork | Num. reflection Rwork | Rfactor Rfree error | Num. reflection all | Num. reflection obs | % reflection obs (%) |
---|
2.8-2.93 | 0.353 | 231 | 9.8 | 0.325 | 2123 | 0.023 | 2637 | 2354 | 89.2 | 2.93-3.08 | 0.354 | 243 | 10.1 | 0.306 | 2161 | 0.023 | 2630 | 2404 | 91.4 | 3.08-3.27 | 0.321 | 271 | 11 | 0.276 | 2199 | 0.019 | 2653 | 2470 | 93.1 | 3.27-3.53 | 0.304 | 240 | 9.6 | 0.251 | 2272 | 0.02 | 2633 | 2512 | 95.4 | 3.53-3.88 | 0.278 | 234 | 9 | 0.22 | 2356 | 0.018 | 2666 | 2590 | 97.1 | 3.88-4.44 | 0.27 | 253 | 9.7 | 0.203 | 2358 | 0.017 | 2688 | 2611 | 97.1 | 4.44-5.59 | 0.242 | 257 | 9.6 | 0.189 | 2416 | 0.015 | 2726 | 2673 | 98.1 | 5.59-34.92 | 0.261 | 279 | 10 | 0.207 | 2523 | 0.016 | 2885 | 2802 | 97.1 |
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | water_rep.paramwater.topX-RAY DIFFRACTION | 3 | | ly_jlm.topX-RAY DIFFRACTION | 4 | | sah.top | | | | | |
|
---|
ソフトウェア | *PLUS 名称: CNS / 分類: refinement |
---|
精密化 | *PLUS 最高解像度: 2.8 Å / 最低解像度: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226 |
---|
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_d0.01 | X-RAY DIFFRACTION | c_angle_deg1.54 | X-RAY DIFFRACTION | c_mcbond_it | X-RAY DIFFRACTION | c_scbond_it | X-RAY DIFFRACTION | c_mcangle_it | X-RAY DIFFRACTION | c_scangle_it | | | | | | |
|
---|