negative regulation of cytokine production => GO:0001818 / positive regulation of protein catabolic process in the vacuole / protein localization to lysosome / protein deubiquitination / RING-type E3 ubiquitin transferase / regulation of protein stability / ubiquitin protein ligase activity / Ovarian tumor domain proteases / late endosome / ubiquitin-dependent protein catabolic process ...negative regulation of cytokine production => GO:0001818 / positive regulation of protein catabolic process in the vacuole / protein localization to lysosome / protein deubiquitination / RING-type E3 ubiquitin transferase / regulation of protein stability / ubiquitin protein ligase activity / Ovarian tumor domain proteases / late endosome / ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / cytoskeleton / Ub-specific processing proteases / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能
解像度: 2.1→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.377 / SU ML: 0.089 / 交差検証法: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
Rfactor
反射数
%反射
Selection details
Rfree
0.2183
927
5.1 %
RANDOM
Rwork
0.19461
-
-
-
obs
0.19576
17299
99.99 %
-
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 32.997 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.75 Å2
0 Å2
0 Å2
2-
-
0.75 Å2
0 Å2
3-
-
-
-1.5 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.1→25 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1286
0
14
142
1442
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
1372
X-RAY DIFFRACTION
r_angle_refined_deg
1.768
1.94
1884
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.195
5
176
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.432
24.259
54
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.762
15
198
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.775
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
211
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1064
X-RAY DIFFRACTION
r_mcbond_it
0.701
1.5
864
X-RAY DIFFRACTION
r_mcangle_it
1.287
2
1403
X-RAY DIFFRACTION
r_scbond_it
2.084
3
508
X-RAY DIFFRACTION
r_scangle_it
3.365
4.5
480
LS精密化 シェル
解像度: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.319
79
-
Rwork
0.288
1239
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 32.9688 Å / Origin y: 14.9519 Å / Origin z: 16.7889 Å