5VY4
Thermoplasma acidophilum 20S Proteasome using 200keV with image shift
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.277 |
f_angle_d | 1.014 |
f_chiral_restr | 0.061 |
f_bond_d | 0.012 |
f_plane_restr | 0.006 |
Sample |
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Thermoplasma acidophilum 20S proteasome |
Specimen Preparation | |
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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 | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 96254 |
Reported Resolution (Å) | 3.3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | D7 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | Maximum Likelihood | ||||
Overall B Value | 99 | ||||
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 ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 65 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 111184 | Template-based particle picking was performed using templates generated from reference-free 2D classification of an initial set of automated particle picks. |