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_long_range_B_refined | 34.865 |
| r_dihedral_angle_2_deg | 32.895 |
| r_dihedral_angle_3_deg | 20.443 |
| r_scbond_it | 19.08 |
| r_dihedral_angle_4_deg | 17.273 |
| r_mcangle_it | 16.586 |
| r_mcbond_it | 11.828 |
| r_dihedral_angle_1_deg | 7.142 |
| r_angle_refined_deg | 2.217 |
| r_chiral_restr | 0.148 |
| 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 | 129446 |
| Reported Resolution (Å) | 2.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | There is very strong preferred orientation that generates a number of problems, in addition to high level of aberrations. |
| 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) | 90 | ||||||||
| 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 | |
| MODEL REFINEMENT | REFMAC | |
| INITIAL EULER ASSIGNMENT | cisTEM | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 236091 | |||
