9HMW | pdb_00009hmw

Structure of the Arabidopsis thaliana 80S ribosome OVAC mutant in complex with P- and E-site tRNAs and mRNA


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it23.713
r_lrange_other23.713
r_dihedral_angle_3_deg18.036
r_dihedral_angle_6_deg15.024
r_scangle_it13.736
r_scangle_other13.736
r_mcangle_it13.12
r_mcangle_other13.12
r_scbond_it8.445
r_scbond_other8.445
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it23.713
r_lrange_other23.713
r_dihedral_angle_3_deg18.036
r_dihedral_angle_6_deg15.024
r_scangle_it13.736
r_scangle_other13.736
r_mcangle_it13.12
r_mcangle_other13.12
r_scbond_it8.445
r_scbond_other8.445
r_mcbond_it8.26
r_mcbond_other8.26
r_dihedral_angle_1_deg5.456
r_dihedral_angle_2_deg4.48
r_angle_refined_deg1.24
r_dihedral_angle_other_2_deg0.682
r_angle_other_deg0.427
r_xyhbond_nbd_refined0.234
r_symmetry_nbd_other0.22
r_nbtor_refined0.219
r_nbd_refined0.19
r_ncsr_local_group_10.182
r_metal_ion_refined0.179
r_symmetry_xyhbond_nbd_other0.127
r_symmetry_nbtor_other0.084
r_chiral_restr0.054
r_chiral_restr_other0.046
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.001
r_bond_other_d
Sample
Ribosome in complex with P- and E-site tRNAs, mRNA, nascent peptide, and thermospermine molecules
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles58638
Reported Resolution (Å)2.25
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 TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)53.85
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)1800
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 SELECTIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION