6OPO | pdb_00006opo

Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VN3

Sample
HIV-1 Env B41 SOSIP in complex with soluble CD4, 17b Fab and DDM

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	183480
Reported Resolution (Å)	3.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Resolution estimated by convergence between CryoSparc2 loose mask value, and by applying the same CryoSparc2 mask and half maps in Relion PostProcess.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (5VN3)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	58

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	22500
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	Leginon
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.13.1
MODEL FITTING	Coot	0.9-pre
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	Coot	0.9-pre
INITIAL EULER ASSIGNMENT	cryoSPARC	2
FINAL EULER ASSIGNMENT	cryoSPARC	2
CLASSIFICATION	cryoSPARC	2
RECONSTRUCTION	cryoSPARC	2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION