9GHG | pdb_00009ghg

Staphylococcus aureus FusB bound to the small subunit of the S. aureus 70S ribosome (FusB-Sa70S:SSU)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8P2F 
in silico modelAlphaFold 
experimental modelPDB 4ADN 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.896
r_dihedral_angle_2_deg7.13
r_dihedral_angle_6_deg6.759
r_lrange_it5.182
r_lrange_other5.147
r_dihedral_angle_1_deg4.791
r_mcangle_it2.854
r_mcangle_other2.854
r_scangle_it2.286
r_scangle_other2.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.896
r_dihedral_angle_2_deg7.13
r_dihedral_angle_6_deg6.759
r_lrange_it5.182
r_lrange_other5.147
r_dihedral_angle_1_deg4.791
r_mcangle_it2.854
r_mcangle_other2.854
r_scangle_it2.286
r_scangle_other2.286
r_mcbond_it1.523
r_mcbond_other1.523
r_scbond_it1.239
r_scbond_other1.239
r_angle_refined_deg0.72
r_dihedral_angle_other_2_deg0.58
r_angle_other_deg0.29
r_nbtor_refined0.223
r_symmetry_nbd_other0.2
r_ncsr_local_group_10.174
r_nbd_refined0.141
r_xyhbond_nbd_refined0.108
r_metal_ion_refined0.105
r_symmetry_nbtor_other0.071
r_symmetry_xyhbond_nbd_other0.047
r_chiral_restr_other0.037
r_chiral_restr0.03
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_gen_planes_other0.001
r_bond_other_d
Sample
FusB on 70S ribosomes
Sample Components
FusB
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles67441
Reported Resolution (Å)2.22
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (8P2F, 4ADN)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)28.14
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)1300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.4.1
MODEL FITTINGCoot0.9.8.92
INITIAL EULER ASSIGNMENTcryoSPARC4.4.1
FINAL EULER ASSIGNMENTcryoSPARC4.4.1
CLASSIFICATIONcryoSPARC4.4.1
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTServalcat
MODEL REFINEMENTCoot0.9.8.92
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION859410