ELECTRON MICROSCOPY

Sample

Retromer-Vps5 complex assembled on the membrane.

Specimen Preperation
Sample Aggregation State 3D ARRAY
Vitrification Instrument LEICA EM GP
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 16037
Reported Resolution (Å) 11.4
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Note that the associated PDB model was not generated by fitting into this map! It was generated by fitting into the associated local high-resolution maps and then combined. Initial global ridgid body fitting was done using Chimera, followed by MDFF within NAMD for flexible fitting. Note that side chain positions are not reliable in model generated by refinement into a map at this resolution.
Data Acquisition
Detector Type GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å2) 3.17
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 2500
Maximum Defocus (nm) 6500
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 105000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION SerialEM 4.8
CTF CORRECTION CTFFIND 4
CTF CORRECTION IMOD ?
MODEL FITTING UCSF Chimera ?
FINAL EULER ASSIGNMENT AV3 ?
FINAL EULER ASSIGNMENT TOM ?
MODEL REFINEMENT NAMD ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction was performed with ctfphaseflip IMOD command using defocus values measured by CTFFIND4 on non-dose-filtered images.