negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol 類似検索 - 分子機能
解像度: 1.9→25.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.258 / SU ML: 0.124 / 交差検証法: THROUGHOUT / ESU R Free: 0.181 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.26865
867
10 %
RANDOM
Rwork
0.21136
-
-
-
all
0.21702
8702
-
-
obs
0.21702
7817
98.68 %
-
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: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 27.027 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.06 Å2
0 Å2
0 Å2
2-
-
0.2 Å2
0 Å2
3-
-
-
-0.14 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→25.22 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
820
0
16
50
886
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
881
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
772
X-RAY DIFFRACTION
r_angle_refined_deg
1.533
1.962
1191
X-RAY DIFFRACTION
r_angle_other_deg
0.643
3
1816
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.8
5
103
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.942
24
45
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.785
15
151
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.89
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
125
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
946
X-RAY DIFFRACTION
r_gen_planes_other
0
0.02
181
X-RAY DIFFRACTION
r_mcbond_it
1.765
3
502
X-RAY DIFFRACTION
r_mcbond_other
0.637
3
201
X-RAY DIFFRACTION
r_mcangle_it
2.582
4
825
X-RAY DIFFRACTION
r_scbond_it
1.97
3
379
X-RAY DIFFRACTION
r_scangle_it
2.822
4
362
LS精密化 シェル
解像度: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.361
69
-
Rwork
0.252
578
-
obs
-
578
98.33 %
精密化 TLS
手法: refined / Origin x: -4.7211 Å / Origin y: 13.1994 Å / Origin z: -14.7708 Å