9QQQ | pdb_00009qqq

Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined16.726
r_long_range_B_other16.673
r_dihedral_angle_3_deg13.434
r_scangle_other13.105
r_mcangle_it12.487
r_mcangle_other12.487
r_scbond_it8.481
r_scbond_other8.473
r_mcbond_it8.363
r_mcbond_other8.363
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined16.726
r_long_range_B_other16.673
r_dihedral_angle_3_deg13.434
r_scangle_other13.105
r_mcangle_it12.487
r_mcangle_other12.487
r_scbond_it8.481
r_scbond_other8.473
r_mcbond_it8.363
r_mcbond_other8.363
r_dihedral_angle_1_deg7.525
r_dihedral_angle_2_deg2.857
r_angle_refined_deg1.137
r_angle_other_deg0.425
r_chiral_restr0.05
r_gen_planes_refined0.012
r_bond_refined_d0.007
r_gen_planes_other0.002
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
Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles343986
Reported Resolution (Å)2.26
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)1.14
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)5000
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
PARTICLE SELECTIONcrYOLO1.9.7
MODEL REFINEMENTREFMAC5.8.0425
RECONSTRUCTIONRELION5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION