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Cryo-EM structure of the NAIP5-NLRC4-flagellin inflammasome
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
10.157
f_angle_d
1.013
f_chiral_restr
0.051
f_plane_restr
0.006
f_bond_d
0.004
Sample
NAIP5-NLRC4-flagellin inflammasome
Sample Components
NAIP5
NLRC4
flagellin
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK II
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
252214
Reported Resolution (Å)
5.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Correlation coefficient
Overall B Value
167
Fitting Procedure
Details
Homology models predicted by I-TASSER server were used as initial model sources. The main structural template identified by I-TASSER for NAIP5 was the ...
Homology models predicted by I-TASSER server were used as initial model sources. The main structural template identified by I-TASSER for NAIP5 was the crystal structure of NLRC4 in the inactive conformation (PDB ID: 4KXF) that covered all the domains except the N-terminal BIR region, where homology models from several BIR domains were recognized (PDB IDs: 1SE0, 2VM5, and 1OXQ for BIR1, BIR2, and BIR3, respectively). Predictions were first rigid body docked into the density map using Chimera and/or ADP_EM. Then, the docked models were flexibly fitted with iMODFIT, if necessary. Finally, all models were refined in Phenix.