5FOJ

Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.331
f_angle_d	0.825
f_chiral_restr	0.052
f_bond_d	0.009
f_plane_restr	0.006

Sample
Grapevine fanleaf virus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3246. (DEPOSITION ID: 14064).
Refinement Type
Symmetry Type
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (4V5T)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial atomic model building was done by a rigid body fitting, followed by extensive manual model building in Coot and real space refinement of the a ...	Initial atomic model building was done by a rigid body fitting, followed by extensive manual model building in Coot and real space refinement of the atomic model against the experimental map using Phenix including restrained temperature factor refinement.

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	6000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	120000
Calibrated Magnification	127272
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Cs-corrected microscope

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
CTF CORRECTION	IMAGIC
RECONSTRUCTION	IMAGIC
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.