ELECTRON MICROSCOPY

Sample

Alpha-mannosidase 1

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details 2.5 ul of sample was applied, offset -3, 9s blotting time
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 33588
Reported Resolution (Å) 6.3
Resolution Method FSC 0.143 CUT-OFF
Other Details 1. From 85274 initially auto-picked particles, 16678 were eliminated after 2D classification. 2. From 68596, two classes making up 33588 particles were included in the final reconstruction.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value 80
Fitting Procedure ?
Details 1. Fitting of a homology model based on PDB 2wyh combined with a homology model based on PDB 2xbz and 3cmg for the C- (residues 287-1083) and N-terminal part (residues 45-203) respectively 2. ab initio modelling for a three-helix bundle of the N-terminal part (residues 209-286) 3. creating an ideal poly-alanine helix for residues 17-27
Data Acquisition
Detector Type FEI FALCON II (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) 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 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 1.3
IMAGE ACQUISITION EPU 1
CTF CORRECTION CTFFIND 3
CTF CORRECTION RELION 1.3
MODEL FITTING UCSF Chimera 8.6
INITIAL EULER ASSIGNMENT EMAN 2.06
FINAL EULER ASSIGNMENT RELION 1.3
CLASSIFICATION RELION 1.3
RECONSTRUCTION RELION 1.3
MODEL REFINEMENT DireX v0.5
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?