6YNG
MicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5G0Z |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.657 | α = 90 |
b = 103.657 | β = 90 |
c = 103.657 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | 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 | 0.226 | 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 | |
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Software Name | Purpose |
PHENIX | refinement |
Sample |
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Cydia pomonella granulosis virus (isolate Mexican) |
Specimen Preparation | |
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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 | |
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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 ... |
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 |
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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 |