6V20

Rabbit muscle aldolase determined using single-particle cryo-EM at 200 keV


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VY5 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.759
f_angle_d0.841
f_chiral_restr0.06
f_bond_d0.01
f_plane_restr0.006
Sample
Aldolase from rabbit muscle
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles394294
Reported Resolution (Å)2.13
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (5VY5)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value30
Fitting Procedure
DetailsStarting model was generated by stripping PDB entry 5VY5 of all ligands and alternate conformations, then refining into the EM density using imposed s ...Starting model was generated by stripping PDB entry 5VY5 of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)67
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)300
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification73000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon3.2
CTF CORRECTIONGctf1.06
MODEL FITTINGUCSF Chimera1.11.2
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.0
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.14_3260
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1801738