6CRR | pdb_00006crr

CryoEM structure of human enterovirus D68 full native virion (pH 7.2 and 4 degrees Celsius)

ELECTRON MICROSCOPY

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Sample
Enterovirus D68

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	10000
Reported Resolution (Å)	3.24
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Correlation coefficient
Overall B Value
Fitting Procedure
Details	A combination of the following approaches was used: (1) model rebuilding using Coot, (2) real space refinement using Phenix, (3) reciprocal space refinment using REFMAC5 (as in standard crystallographic refinement).

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	5900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	18000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN2
PARTICLE SELECTION	DoG Picker
IMAGE ACQUISITION	Leginon	3.2
CTF CORRECTION	jspr
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
MODEL REFINEMENT	REFMAC
INITIAL EULER ASSIGNMENT	jspr
FINAL EULER ASSIGNMENT	jspr
CLASSIFICATION	RELION	2.0.5
RECONSTRUCTION	jspr

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	On-the-fly CTF correction during 2D alignment and 3D reconstruction	264850