5VY3
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 ... | ||||
| 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. | ||
