6WXF | pdb_00006wxf

Cryo-EM reconstruction of VP5*/VP8* assembly from rhesus rotavirus particles - Intermediate conformation

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V7Q
experimental model	PDB	1SLQ

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.5409
f_angle_d	0.6828
f_chiral_restr	0.0443
f_plane_restr	0.0044
f_bond_d	0.0037

Sample
Rotavirus VP4, VP6, VP7 assembly in an intermediate confromattion

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details	4 ul sample volume, 4 sec blotting time

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	82008
Reported Resolution (Å)	4.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Reconstruction final map after classification of VP4 sub-particles . VP4 sub-particles extracted from viral particles (60 VP4 sub-particles per viral particle)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4V7Q, 1SLQ)
Refinement Space
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	phenix.real_space_refine

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	33

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	27500
Calibrated Magnification	40605
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf
MODEL FITTING	O
MODEL REFINEMENT	PHENIX	1.17.1-3660
INITIAL EULER ASSIGNMENT	cisTEM
FINAL EULER ASSIGNMENT	cisTEM
CLASSIFICATION	cisTEM
RECONSTRUCTION	cisTEM

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3522	whole viral particles