Experiment: 8VWH

Structure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)

ELECTRON MICROSCOPY

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	4.484
f_angle_d	0.451
f_chiral_restr	0.041
f_bond_d	0.003
f_plane_restr	0.003

Sample
Autographa californica multiple nucleopolyhedrovirus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Grid was blotted using zero incubation time, blot time of 2 s, blot force of -10 and drain time of 1 s.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1002951
Reported Resolution (Å)	3.06
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final reconstruction was generated using local refinement in cryoSPARC.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	ChimeraX was used to perform rigid-body fitting of an AlphaFold2 model. Flexible modeling was performed using Coot and refined in Phenix.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	47.3

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1200
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
PARTICLE SELECTION	cryoSPARC	4.1.2
PARTICLE SELECTION	EMAN2	2.2
PARTICLE SELECTION	RELION	2.1
IMAGE ACQUISITION	EPU	1
CTF CORRECTION	cryoSPARC	4.1.2
MODEL FITTING	UCSF ChimeraX	1.5
MODEL FITTING	Coot	0.9.8.6
MODEL REFINEMENT	PHENIX	1.20.1_4487
INITIAL EULER ASSIGNMENT	SPRING	0.84.1470
INITIAL EULER ASSIGNMENT	RELION	2.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.1.2
CLASSIFICATION	cryoSPARC	4.1.2
RECONSTRUCTION	cryoSPARC	4.1.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE	Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction	2165694	Manually selected particles in EMAN2 were used to create a 2D template in cryoSPARC for automated filament tracing resulting in 77,356 particles. After helical refinement and symmetry expansion, 2,165,694 subparticles were extracted.