Single particle reconstruction of HemQ from Geobacillus based on data acquired in the presence of substantial aberrations
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1T0T | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.772 |
| r_long_range_B_refined | 31.106 |
| r_dihedral_angle_3_deg | 19.637 |
| r_mcangle_it | 18.53 |
| r_scbond_it | 17.99 |
| r_dihedral_angle_4_deg | 16.596 |
| r_mcbond_it | 14.196 |
| r_dihedral_angle_1_deg | 6.794 |
| r_angle_refined_deg | 2.074 |
| r_chiral_restr | 0.138 |
| Sample |
|---|
| HemQ |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 81302 |
| Reported Resolution (Å) | 2.32 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C5 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1T0T) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | REFMAC | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | COOT was crucial as well. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 120 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS TALOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | The goal of the experiment was to show that it is possible to perform high resolution reconstruction in the presence of higher order aberrations. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cisTEM | |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cisTEM | |
| MODEL FITTING | MOLREP | |
| INITIAL EULER ASSIGNMENT | cisTEM | |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 156210 | |||
