9H90 | pdb_00009h90

Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other16.684
r_long_range_B_refined16.683
r_dihedral_angle_3_deg13.98
r_scangle_other11.455
r_dihedral_angle_2_deg11.378
r_mcangle_other10.46
r_mcangle_it10.459
r_dihedral_angle_1_deg8.521
r_scbond_it6.794
r_scbond_other6.793
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other16.684
r_long_range_B_refined16.683
r_dihedral_angle_3_deg13.98
r_scangle_other11.455
r_dihedral_angle_2_deg11.378
r_mcangle_other10.46
r_mcangle_it10.459
r_dihedral_angle_1_deg8.521
r_scbond_it6.794
r_scbond_other6.793
r_mcbond_it6.244
r_mcbond_other6.24
r_angle_refined_deg1.109
r_angle_other_deg0.419
r_chiral_restr0.051
r_gen_planes_refined0.01
r_bond_refined_d0.007
r_gen_planes_other0.003
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Structure of the Vibrio natriegens 30S ribosomal subunit in complex with spectinomycin
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles294068
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)1200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0425
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION