Experiment: 9IKC

Orf virus scaffolding protein Orfv075

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VFD

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.456
f_angle_d	0.463
f_chiral_restr	0.045
f_plane_restr	0.004
f_bond_d	0.002

Sample
Orfv075 trimer

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	714562
Reported Resolution (Å)	1.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (7VFD)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Structure of orthologue protein D13 (PDB 7VFD) was fitted into the density map of orfv075 using UCSF Chimera. The fitted structure was modified in Coo ...	Structure of orthologue protein D13 (PDB 7VFD) was fitted into the density map of orfv075 using UCSF Chimera. The fitted structure was modified in Coot based on sequence alignment between D13 and Orfv075. The resulting Orfv075 model was refined using PHENIX.

Data Acquisition
Detector Type	GATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	1800
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	130000
Calibrated Magnification	76923
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4.1
IMAGE ACQUISITION	EPU	3.6
CTF CORRECTION	cryoSPARC	4.4.1
MODEL FITTING	Coot	0.9.8.92
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
RECONSTRUCTION	cryoSPARC	4.4.1
MODEL REFINEMENT	PHENIX	1.21

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2051025