5MDY | pdb_00005mdy

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.34
r_dihedral_angle_1_deg27.595
r_dihedral_angle_3_deg18.892
r_dihedral_angle_4_deg16.317
r_long_range_B_refined14.523
r_long_range_B_other14.523
r_mcangle_it7.894
r_mcangle_other7.894
r_scangle_other5.964
r_mcbond_it4.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.34
r_dihedral_angle_1_deg27.595
r_dihedral_angle_3_deg18.892
r_dihedral_angle_4_deg16.317
r_long_range_B_refined14.523
r_long_range_B_other14.523
r_mcangle_it7.894
r_mcangle_other7.894
r_scangle_other5.964
r_mcbond_it4.354
r_mcbond_other4.354
r_scbond_it3.379
r_scbond_other3.379
r_angle_other_deg1.342
r_angle_refined_deg1.224
r_chiral_restr0.238
r_gen_planes_refined0.007
r_bond_refined_d0.006
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
Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles54465
Reported Resolution (Å)3.35
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 Value75.3
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)48
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification134615
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
MODEL FITTINGCoot0.8.7
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 CORRECTION