5YRN | pdb_00005yrn

Structure of RIP2 CARD domain

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.673
f_angle_d	0.881
f_chiral_restr	0.051
f_bond_d	0.007
f_plane_restr	0.005

Sample
Active RIP2 signaling complex

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument
Cryogen Name	METHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	142330
Reported Resolution (Å)	4.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Model building was based on a cropped-out density segment. Pseudo-crystallographic refinement showed that the central segment of the map is good until 3.5-3.7 A.
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	4.936
Angular Rotation	-101.373

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Rfree value
Overall B Value	202.7
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	8

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

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	RELION	2.0beta
CTF CORRECTION	RELION	2.0beta
MODEL FITTING	PHENIX	1.13
INITIAL EULER ASSIGNMENT	RELION	2.0beta
FINAL EULER ASSIGNMENT	RELION	2.0beta
CLASSIFICATION	RELION	2.0beta
RECONSTRUCTION	RELION	2.0beta
MODEL REFINEMENT	Coot	0.8.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		658160