5MLC

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.841
r_dihedral_angle_1_deg23.871
r_long_range_B_refined22.48
r_long_range_B_other22.48
r_dihedral_angle_3_deg21.82
r_dihedral_angle_4_deg17.696
r_mcangle_it13.726
r_mcangle_other13.726
r_scangle_other12.489
r_mcbond_it8.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.841
r_dihedral_angle_1_deg23.871
r_long_range_B_refined22.48
r_long_range_B_other22.48
r_dihedral_angle_3_deg21.82
r_dihedral_angle_4_deg17.696
r_mcangle_it13.726
r_mcangle_other13.726
r_scangle_other12.489
r_mcbond_it8.128
r_mcbond_other8.127
r_scbond_it7.459
r_scbond_other7.459
r_angle_refined_deg1.799
r_angle_other_deg1.526
r_chiral_restr0.17
r_bond_refined_d0.013
r_gen_planes_refined0.01
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
50S subunit of the spinach chloroplast ribosome
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles37636
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
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)2.6
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 Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION