7QEP
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.5906 |
f_angle_d | 0.9431 |
f_chiral_restr | 0.0529 |
f_bond_d | 0.0089 |
f_plane_restr | 0.0058 |
Sample |
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Ribosome from Encephalitozoon cuniculi |
Sample Components |
large subunit |
small subunit |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Quantifoil grids (R1.2/1.3, 400 mesh, copper) were glow discharged (10 mA, 30s, Quorum GloQube), and 3 microlitres of the crude sample of E. cuniculi ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 108005 |
Reported Resolution (Å) | 2.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | The remaining particles were re-extracted without binning and aligned and refined in 3D, again using a 60 Angstrom low-passed filtered ab initio start ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (4V88, 6RM3) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | The model was built using fragments of S. cerevisiae (pdb id 4v88) and V. necatrix ribosomes (pdb id 6rm3) as starting models that were edited using C ... |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2600 |
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 | 96000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | RELION | 3.1 |
CTF CORRECTION | CTFFIND | 4.1 |
MODEL FITTING | Coot | 0.9 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX | 1.14 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 260895 | Particles were picked using Laplacian-of-Gaussian autopicking and reference-free 2D classification used to generate templates for further autopicking. The resulting particles were extracted with binning-by-4, and 2D and 3D classification performed to remove junk images |