5LZU | pdb_00005lzu

Structure of the mammalian ribosomal termination complex with accommodated eRF1


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.907
r_dihedral_angle_1_deg29.718
r_long_range_B_refined23.416
r_long_range_B_other23.416
r_dihedral_angle_3_deg16.68
r_dihedral_angle_4_deg13.74
r_mcangle_it9.075
r_mcangle_other9.075
r_scangle_other7.553
r_mcbond_it5.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.907
r_dihedral_angle_1_deg29.718
r_long_range_B_refined23.416
r_long_range_B_other23.416
r_dihedral_angle_3_deg16.68
r_dihedral_angle_4_deg13.74
r_mcangle_it9.075
r_mcangle_other9.075
r_scangle_other7.553
r_mcbond_it5.109
r_mcbond_other5.109
r_scbond_it4.333
r_scbond_other4.333
r_angle_other_deg1.18
r_angle_refined_deg1.102
r_chiral_restr0.133
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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
Affinity-purified 80S ribosome-nascent chain complex reconstituted with eRF1.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles13852
Reported Resolution (Å)3.75
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement TargetFSCaverage
Overall B Value63.8
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)30
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification59000
Calibrated Magnification104478
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf0.5
MODEL FITTINGUCSF Chimera1.10
MODEL FITTINGCoot5.8
MODEL REFINEMENTREFMAC5.8
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION105812