Experiment: 6YNG

MicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0Z

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.657	α = 90
b = 103.657	β = 90
c = 103.657	γ = 90

Symmetry
Space Group	I 2 3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	THROUGHOUT	5G0Z	2.8	2.8	1.39	4004	400	88	0.1883	0.1845	0.2157	0.226	0.2707	Random selection

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.655
f_angle_d	0.83
f_chiral_restr	0.05
f_plane_restr	0.005
f_bond_d	0.004

Software

Software
Software Name	Purpose
PHENIX	refinement

Sample
Cydia pomonella granulosis virus (isolate Mexican)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	NITROGEN
Sample Vitrification Details	3 s blot, 0.5 s draining
Embedding Material	Ice
Embedding Details	Undiluted sample was applied to glow-discharged 200 mesh copper Quantifoil.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	2.8
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details	RESOLUTION OF MERGED DATASET DEFINED BY AN INSCRIBED CIRCLE ON THE CAMERA SURFACE, WAS LIMITED 3.0 TO BY THE CAMERA TO SAMPLE DISTANCE. DATA INTEGRAT ...	RESOLUTION OF MERGED DATASET DEFINED BY AN INSCRIBED CIRCLE ON THE CAMERA SURFACE, WAS LIMITED 3.0 TO BY THE CAMERA TO SAMPLE DISTANCE. DATA INTEGRATED WITH DIALS, COMBINED WITH POINTLESS, AND SCALED WITH AIMLESS. INTENSITIES CONVERTED TO STRUCTURE FACTOR AMPLITUDES WITH STARANISO. INITIAL PHASES DETERMINED BY RIGID BODY FITTING A MODEL DERIVED FROM PDB ENTRY 5G0Z IN PHENIX.REFINE. FINAL REFINEMENT CARRIED OUT IN PHENIX.REFINE
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	103.66
Length b	103.66
Length c	103.66
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (5G0Z)
Refinement Space	RECIPROCAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)	1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE