ELECTRON MICROSCOPY

Sample

human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a

Specimen Preperation
Sample Aggregation State 3D ARRAY
Vitrification Instrument FEI VITROBOT MARK I
Cryogen Name ETHANE
Sample Vitrification Details Blot force 20, blot time 6 s
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 26979
Reported Resolution (Å) 9.8
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 correlation
Overall B Value 320
Fitting Procedure ?
Details An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 2.99
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 2000
Maximum Defocus (nm) 5000
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 81000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
VOLUME SELECTION MATLAB R2016b
IMAGE ACQUISITION SerialEM 3.8
CTF CORRECTION NOVACTF 1.0.0
MODEL FITTING Coot 0.9
MODEL FITTING ISOLDE 1.1
FINAL EULER ASSIGNMENT MATLAB R2016b
CLASSIFICATION MATLAB R2016b
RECONSTRUCTION RELION 3.1
MODEL REFINEMENT REFMAC 5.8.0272
MODEL REFINEMENT ISOLDE 1.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?