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 ... |
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 ... |
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 |