5M3L
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.793 |
| r_long_range_B_refined | 23.064 |
| r_long_range_B_other | 23.064 |
| r_scangle_other | 15.712 |
| r_mcangle_it | 13.938 |
| r_mcangle_other | 13.937 |
| r_dihedral_angle_3_deg | 12.167 |
| r_dihedral_angle_4_deg | 12.076 |
| r_scbond_it | 9.482 |
| r_scbond_other | 9.482 |
| Sample |
|---|
| Giant worm hemoglobin |
| 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 | 75000 |
| Reported Resolution (Å) | 3.8 |
| Resolution Method | FSC 1/2 BIT CUT-OFF |
| Other Details | FSC as per the original definition (Harauz & van Heel 1986). |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D6 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 1200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.02 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | 59000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | IMAGIC-4D | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | IMAGIC-4D | |
| MODEL FITTING | UCSF Chimera | 1.11 |
| MODEL REFINEMENT | REFMAC | 5.8.0155 |
| MODEL REFINEMENT | PHENIX | 1.10.1 |
| MODEL REFINEMENT | Coot | 0.8.6 |
| INITIAL EULER ASSIGNMENT | IMAGIC-4D | |
| FINAL EULER ASSIGNMENT | IMAGIC-4D | |
| CLASSIFICATION | IMAGIC-4D | |
| RECONSTRUCTION | IMAGIC-4D | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | Unsupervised MSA classification of amplitude spectra throughout the full data set ("Full data set CTF correction") | 319746 | ||
