8V9L | pdb_00008v9l

Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O61

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.668
f_angle_d	0.673
f_chiral_restr	0.042
f_bond_d	0.006
f_plane_restr	0.006

Sample
Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	101909
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5o61)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40.12

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.2.1
IMAGE ACQUISITION	SerialEM
MASKING	cryoSPARC	4.2.1
CTF CORRECTION	cryoSPARC	4.2.1
MODEL FITTING	UCSF Chimera	1.14
MODEL REFINEMENT	PHENIX	1.19.2.4158
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.1
CLASSIFICATION	cryoSPARC	4.2.1
RECONSTRUCTION	cryoSPARC	4.2.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION