8YT4
Structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy to 1.42 Angstrom Resolution
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1HQK | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 13.545 |
| r_long_range_B_refined | 6.813 |
| r_long_range_B_other | 6.792 |
| r_dihedral_angle_1_deg | 5.613 |
| r_scangle_other | 5.075 |
| r_dihedral_angle_2_deg | 3.66 |
| r_scbond_it | 3.144 |
| r_scbond_other | 3.144 |
| r_mcangle_it | 1.917 |
| r_mcangle_other | 1.893 |
| Sample |
|---|
| Lumazine synthase |
| 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 | 470878 |
| Reported Resolution (Å) | 1.42 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1HQK) | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 46 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 1200 |
| 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 | 270000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | 3.5.1 |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | RELION | 5 |
| FINAL EULER ASSIGNMENT | RELION | 5 |
| CLASSIFICATION | RELION | 5 |
| RECONSTRUCTION | RELION | 5 |
| MODEL REFINEMENT | REFMAC | 5.8.0405 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 698240 | |||
