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 |
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Giant worm hemoglobin |
Specimen Preparation | |
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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 |
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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 |