7QCA
Spraguea lophii ribosome
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6RM3 |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.398 |
r_lrange_it | 22.782 |
r_dihedral_angle_4_deg | 18.691 |
r_dihedral_angle_3_deg | 13.407 |
r_mcangle_it | 11.11 |
r_scangle_it | 10.336 |
r_dihedral_angle_1_deg | 7.116 |
r_mcbond_it | 6.445 |
r_scbond_it | 6.373 |
r_angle_refined_deg | 1.832 |
Sample |
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Ribosome |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | blot force -1 and blot time 4 s |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 285940 |
Reported Resolution (Å) | 2.79 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6RM3) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
Electron Dose (electrons/Å**2) | 41.5 | 41.34 |
Imaging Experiment | 1 | 2 |
---|---|---|
Date of Experiment | ||
Temperature (Kelvin) | ||
Microscope Model | TFS KRIOS | TFS TALOS |
Minimum Defocus (nm) | 1200 | 1200 |
Maximum Defocus (nm) | 2500 | 2500 |
Minimum Tilt Angle (degrees) | ||
Maximum Tilt Angle (degrees) | ||
Nominal CS | ||
Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
Specimen Holder Model | ||
Nominal Magnification | ||
Calibrated Magnification | ||
Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | Warp | 1.09 |
MODEL FITTING | Coot | |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | UCSF ChimeraX | |
MODEL FITTING | MOLREP | |
MODEL REFINEMENT | REFMAC | |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
IMAGE ACQUISITION | EPU |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 977879 |