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Thermoplasma acidophilum 20S Proteasome using 200keV with stage position
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
10.433
f_angle_d
1.106
f_chiral_restr
0.061
f_bond_d
0.01
f_plane_restr
0.006
Sample
Thermoplasma acidophilum 20S proteasome
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
106581
Reported Resolution (Å)
3.1
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
D7
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Maximum Likelihood
Overall B Value
101
Fitting Procedure
Details
Starting model was generated by stripping PDB entry 1YAR of all ligands and alternate conformations, then refining into the EM density using imposed s ...
Starting model was generated by stripping PDB entry 1YAR of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
65
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2800
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
45000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
FindEM
IMAGE ACQUISITION
Leginon
3.2
CTF CORRECTION
CTFFIND
4
CTF CORRECTION
Gctf
1.06
CTF CORRECTION
RELION
1.4
MODEL FITTING
Rosetta
2016.32.5883
MODEL REFINEMENT
PHENIX
1.11.1-2580
INITIAL EULER ASSIGNMENT
RELION
2.0
FINAL EULER ASSIGNMENT
RELION
2.0
RECONSTRUCTION
RELION
2.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
153429
Template-based particle picking was performed using templates generated from reference-free 2D classification of an initial set of automated particle picks.