8PUV | pdb_00008puv

Trimeric prM/E spike of Tick-borne encephalitis virus immature particle

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.129
f_angle_d	0.411
f_chiral_restr	0.042
f_bond_d	0.002
f_plane_restr	0.002

Sample
Tick-borne encephalitis virus

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	552993
Reported Resolution (Å)	4
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	RIGID BODY FIT
Refinement Target	CC
Overall B Value
Fitting Procedure
Details	inital alhafol generated model was rigidbody fitted into map by Chimera, manually adjusted in Coot and realspace refined in Phenix

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.14
MODEL FITTING	Coot	1.9.8
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.20

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1639578	picked as sub-particles form original whole immature particle reconstruction