7BJP | pdb_00007bjp

The cryo-EM structure of vesivirus 2117, an adventitious agent and possible cause of haemorrhagic gastroenteritis in dogs.

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.247
f_angle_d	0.986
f_chiral_restr	0.063
f_bond_d	0.012
f_plane_restr	0.007

Sample
Calicivirus isolate 2117

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Sample was loaded onto C-flat C1.2/1.3 grids bearing a thin continuous carbon film, allowed to adsorb for one minute before blotting for 3 seconds and plunging into liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	15989
Reported Resolution (Å)	3.65
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	DIRECT ELECTRON DE-64 (8k x 8k)
Electron Dose (electrons/Å**2)	55

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	JEOL CRYOSPECPORTER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	JADAS
CTF CORRECTION	Gctf
CTF CORRECTION	RELION	3.0.3
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	3.0.3
FINAL EULER ASSIGNMENT	RELION	3.0.3
CLASSIFICATION	RELION	3.0.3
RECONSTRUCTION	RELION	3.0.3
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	REFMAC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		65071	Automated particle picking was performed using RELION