6EGV | pdb_00006egv

Sacbrood virus of honeybee

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.486
r_dihedral_angle_3_deg	11.677
r_dihedral_angle_4_deg	9.805
r_dihedral_angle_1_deg	5.401
r_long_range_B_refined	1.411
r_long_range_B_other	1.411
r_angle_refined_deg	0.933
r_mcangle_it	0.666
r_mcangle_other	0.666
r_angle_other_deg	0.603
r_mcbond_it	0.349
r_mcbond_other	0.349
r_scangle_other	0.344
r_scbond_it	0.153
r_scbond_other	0.153
r_chiral_restr	0.038
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
Sacbrood virus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	13148
Reported Resolution (Å)	3.18
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	R-factor
Overall B Value	47.1
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	21

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
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	75000
Calibrated Magnification	74325
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage).

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
FINAL EULER ASSIGNMENT	RELION	2
CLASSIFICATION	RELION	2
RECONSTRUCTION	RELION	2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		51000	Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were further reconstructed separately.