9VIN | pdb_00009vin

Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AC5
experimental model	PDB	1ICH
experimental model	PDB	6AC0

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.9052
f_angle_d	0.5461
f_chiral_restr	0.0358
f_plane_restr	0.0051
f_bond_d	0.0031

Sample
Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	68510
Reported Resolution (Å)	3.41
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6AC5, 1ICH, 6ac0)
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.6.2
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	4.6.2
MODEL FITTING	PHENIX	1.20.1
INITIAL EULER ASSIGNMENT	cryoSPARC	4.6.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.6.2
CLASSIFICATION	cryoSPARC	4.6.2
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.20.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		104838