7TCN

Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6UDA 
experimental modelPDB 5F96 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.851
f_angle_d0.809
f_chiral_restr0.051
f_plane_restr0.005
f_bond_d0.004
Sample
Trimeric HIV-1 Env in complex with CH235.12
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification DetailsBLOT FOR 2.5 S BEFORE PLUNGING
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles53398
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (6UDA, 5F96)
Refinement Space
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)66.71
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)750
Maximum Defocus (nm)2500
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
IMAGE ACQUISITIONLatitude
CTF CORRECTIONcryoSPARC
MODEL FITTINGUCSF Chimera
MODEL FITTINGCoot
MODEL FITTINGRosettaEM
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
MODEL REFINEMENTISOLDE
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION