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Model of retromer-Vps5 complex assembled on membrane.
ELECTRON MICROSCOPY
Sample
Retromer-Vps5 complex assembled on the membrane.
Specimen Preparation
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
Point Symmetry
C2
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 m ...
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/Å**2)
3.17
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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.