8UU7
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7NHN |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.002 |
f_angle_d | 0.554 |
f_chiral_restr | 0.035 |
f_plane_restr | 0.005 |
f_bond_d | 0.004 |
Sample |
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Listeria innocua 70S ribosome in complex with HPF, HflXr and E-site tRNA |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 27543 |
Reported Resolution (Å) | 3.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (7NHN) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2300 |
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 |
PARTICLE SELECTION | cryoSPARC | 4.1.2 |
IMAGE ACQUISITION | SerialEM | |
MASKING | cryoSPARC | 4.1.2 |
CTF CORRECTION | cryoSPARC | 4.1.2 |
MODEL FITTING | UCSF Chimera | 1.14 |
MODEL REFINEMENT | PHENIX | 1.19.2.4158 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4.1.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4.1.2 |
CLASSIFICATION | cryoSPARC | 4.1.2 |
RECONSTRUCTION | cryoSPARC | 4.1.2 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |