Experiment: 7K25

Murine polyomavirus hexavalent capsomer, subparticle reconstruction

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SIE
experimental model	PDB	3GK8

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.7761
f_angle_d	0.8732
f_chiral_restr	0.0537
f_bond_d	0.009
f_plane_restr	0.0072

Sample
Murine polyomavirus strain A2

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	929940
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (1SIE, 3GK8)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	Homology model for Fab was generated using SwissModel. Initial models were docked into density in Chimera. Fab CDR loops were manually rebuilt in Coot ...	Homology model for Fab was generated using SwissModel. Initial models were docked into density in Chimera. Fab CDR loops were manually rebuilt in Coot. Iterative rounds of real space refinements (PHENIX) and manual adjustment (coot) were conducted to improve fit to density.

Data Acquisition
Detector Type	FEI FALCON III (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)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF Chimera
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	RELION	3.1

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