8WJ0
cryo-EM structure of human haemoglobin in carbonmonoxy form
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2DN3 |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.015 |
r_dihedral_angle_3_deg | 22.062 |
r_long_range_B_other | 20.161 |
r_long_range_B_refined | 20.143 |
r_scangle_other | 14.365 |
r_scbond_it | 9.356 |
r_scbond_other | 9.348 |
r_mcangle_it | 8.579 |
r_mcangle_other | 8.577 |
r_mcbond_it | 6.348 |
Sample |
---|
human haemoglobin in carbonmonoxy form |
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 | 504650 |
Reported Resolution (Å) | 2.24 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (2dn3) | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
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 | 165000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | 4.2.1 |
MODEL FITTING | Coot | 0.9.8.8 |
MODEL FITTING | ISOLDE | 1.6 |
MODEL FITTING | UCSF ChimeraX | 1.6.1 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
RECONSTRUCTION | cryoSPARC | 4.2.1 |
MODEL REFINEMENT | Servalcat | 0.2.85 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |