9HES | pdb_00009hes

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


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it21.358
r_lrange_other21.358
r_dihedral_angle_3_deg17.76
r_dihedral_angle_6_deg14.527
r_scangle_it12.816
r_scangle_other12.816
r_mcangle_it11.708
r_mcangle_other11.708
r_scbond_it7.952
r_scbond_other7.952
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it21.358
r_lrange_other21.358
r_dihedral_angle_3_deg17.76
r_dihedral_angle_6_deg14.527
r_scangle_it12.816
r_scangle_other12.816
r_mcangle_it11.708
r_mcangle_other11.708
r_scbond_it7.952
r_scbond_other7.952
r_mcbond_it7.533
r_mcbond_other7.533
r_dihedral_angle_1_deg5.653
r_dihedral_angle_2_deg5.059
r_angle_refined_deg1.302
r_dihedral_angle_other_2_deg0.666
r_angle_other_deg0.444
r_nbtor_refined0.219
r_xyhbond_nbd_refined0.218
r_symmetry_nbd_other0.216
r_nbd_refined0.19
r_ncsr_local_group_10.183
r_metal_ion_refined0.161
r_symmetry_xyhbond_nbd_other0.149
r_symmetry_nbtor_other0.084
r_chiral_restr0.057
r_chiral_restr_other0.056
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Particles31655
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
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION