8H0I

Cryo-EM structure of APOBEC3G-Vif complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IR2 
experimental modelPDB 6NIL 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.923
f_angle_d0.539
f_chiral_restr0.042
f_plane_restr0.004
f_bond_d0.002
Sample
A3G-VC-RNA complex
Sample Components
APOVEC3G
Vif
RNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
Embedding MaterialGraphene oxide
Embedding Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles907456
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (3IR2, 6NIL, 6NIL)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)37
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONCTFFIND4.1.9
MODEL FITTINGPHENIX1.19.2
MODEL FITTINGCoot0.8.9.2
INITIAL EULER ASSIGNMENTRELION3.1.3
FINAL EULER ASSIGNMENTRELION3.1.3
CLASSIFICATIONRELION3.1.3
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.19.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2831190