6YNG | pdb_00006yng

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


ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G0Z 

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.657α = 90
b = 103.657β = 90
c = 103.657γ = 90
Symmetry
Space GroupI 2 3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
ELECTRON CRYSTALLOGRAPHYMOLECULAR REPLACEMENTTHROUGHOUT5G0Z2.82.81.394004400880.18830.18450.21570.2260.2707Random 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
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.655
f_angle_d0.83
f_chiral_restr0.05
f_plane_restr0.005
f_bond_d0.004

Software

Software
Software NamePurpose
PHENIXrefinement
Sample
Cydia pomonella granulosis virus (isolate Mexican)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameNITROGEN
Sample Vitrification Details3 s blot, 0.5 s draining
Embedding MaterialIce
Embedding DetailsUndiluted sample was applied to glow-discharged 200 mesh copper Quantifoil.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles
Reported Resolution (Å)2.8
Resolution MethodDIFFRACTION PATTERN/LAYERLINES
Other DetailsRESOLUTION 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 Type3D CRYSTAL
Space Group Name
Length a103.66
Length b103.66
Length c103.66
Angle Alpha90
Angle Beta90
Angle Gamma90
Map-Model Fitting and Refinement
Id1 (5G0Z)
Refinement SpaceRECIPROCAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE