9GHE | pdb_00009ghe

Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S ribosome (FusB-70S:SSU)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8CGK
experimental model	PDB	8CF1
experimental model	PDB	8CGJ
experimental model	PDB	7K00
experimental model	PDB	7N2C

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.854
r_dihedral_angle_6_deg	8.917
r_lrange_it	7.137
r_lrange_other	7.137
r_dihedral_angle_2_deg	6.518
r_dihedral_angle_1_deg	4.989
r_scangle_it	4.618
r_scangle_other	4.618
r_mcangle_it	3.758
r_mcangle_other	3.758
r_scbond_it	2.733
r_scbond_other	2.733
r_mcbond_it	2.121
r_mcbond_other	2.121
r_angle_refined_deg	0.943
r_dihedral_angle_other_2_deg	0.531
r_angle_other_deg	0.324
r_nbtor_refined	0.223
r_symmetry_nbd_other	0.201
r_nbd_refined	0.151
r_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.04
r_symmetry_xyhbond_nbd_other	0.039
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.001
r_bond_other_d

Sample
FusB on 70S ribosomes
Sample Components
FusB
mRNA
70S ribosome

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	349231
Reported Resolution (Å)	1.87
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8CGK, 8CF1, 8CGJ, 7K00, 7N2C)
Refinement Space	REAL
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)	45.47

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	1000
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	4.4.1
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
CLASSIFICATION	cryoSPARC	4.4.1
RECONSTRUCTION	cryoSPARC	4.4.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3613403