ELECTRON MICROSCOPY

Sample

EccB3 dimeric structure from ESX-3/Type VII secretion system

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Blotting time: 3s Blotting force: -10
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 55342
Reported Resolution (Å) 4.6
Resolution Method FSC 0.143 CUT-OFF
Other Details Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target Map correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 50.0
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1600
Maximum Defocus (nm) 2600
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 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION ?
IMAGE ACQUISITION EPU ?
CTF CORRECTION Gctf ?
MODEL FITTING PHENIX 1.14
INITIAL EULER ASSIGNMENT RELION ?
FINAL EULER ASSIGNMENT RELION ?
CLASSIFICATION RELION ?
RECONSTRUCTION RELION ?
MODEL REFINEMENT PHENIX 1.14
MODEL REFINEMENT UCSF Chimera ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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