9H91 | pdb_00009h91

Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17).


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined19.555
r_long_range_B_other19.555
r_scangle_other16.663
r_mcangle_other15.707
r_mcangle_it15.705
r_dihedral_angle_3_deg14.729
r_scbond_it12.687
r_scbond_other12.687
r_mcbond_it12.556
r_mcbond_other12.556
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined19.555
r_long_range_B_other19.555
r_scangle_other16.663
r_mcangle_other15.707
r_mcangle_it15.705
r_dihedral_angle_3_deg14.729
r_scbond_it12.687
r_scbond_other12.687
r_mcbond_it12.556
r_mcbond_other12.556
r_dihedral_angle_2_deg12.297
r_dihedral_angle_1_deg6.819
r_angle_refined_deg1.422
r_angle_other_deg0.541
r_chiral_restr0.063
r_gen_planes_refined0.016
r_bond_refined_d0.01
r_gen_planes_other0.003
r_bond_other_d0.001
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 Proline-rich Antimicrobial Peptide Bac5(1-17) in Complex with the Vibrio natriegens 50S ribosomal subunit
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles294068
Reported Resolution (Å)2.7
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