5JM0

Structure of the S. cerevisiae alpha-mannosidase 1

ELECTRON MICROSCOPY

Sample
Alpha-mannosidase 1

Specimen Preparation
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 wer ...	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
Point Symmetry	D2

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-termin ...	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/Å**2)	58

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		85274

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.