5VN3

ELECTRON MICROSCOPY

Sample

HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details 3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 46855
Reported Resolution (Å) 3.7
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target EMRinger
Overall B Value ?
Fitting Procedure ?
Details Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 58
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 4000
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 38168
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION DoG Picker ?
IMAGE ACQUISITION Leginon ?
CTF CORRECTION Gctf 1.06
MODEL FITTING UCSF Chimera 1.10.1
MODEL REFINEMENT Rosetta 2016.02.58402
MODEL REFINEMENT PHENIX 1.11.1-2575
INITIAL EULER ASSIGNMENT RELION 2.0
FINAL EULER ASSIGNMENT RELION 2.0
CLASSIFICATION RELION 2.0
RECONSTRUCTION RELION 2.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?