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Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.376 r_dihedral_angle_1_deg 27.114 r_long_range_B_refined 23.079 r_long_range_B_other 23.079 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 13.339 r_mcangle_it 7.147 r_mcangle_other 7.147 r_scangle_other 6.08 r_mcbond_it 3.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.376 r_dihedral_angle_1_deg 27.114 r_long_range_B_refined 23.079 r_long_range_B_other 23.079 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 13.339 r_mcangle_it 7.147 r_mcangle_other 7.147 r_scangle_other 6.08 r_mcbond_it 3.999 r_mcbond_other 3.999 r_scbond_it 3.461 r_scbond_other 3.461 r_angle_other_deg 1.147 r_angle_refined_deg 0.999 r_chiral_restr 0.111 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 stalled with didemnin B and containing aminoacyl-tRNA and eEF1A.
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details 3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 40347 Reported Resolution (Å) 3.31 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target FSCaverage Overall B Value 64.8 Fitting Procedure Details Restraints for didemnin B were derived from Phenix.elbow and Mogul.
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 69000 Calibrated Magnification 134615 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION EMAN 2 PARTICLE SELECTION RELION 1.4 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 0.5 MODEL FITTING UCSF Chimera 1.10 MODEL FITTING Coot 5.8 INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 CLASSIFICATION RELION 1.4 RECONSTRUCTION RELION 1.4 MODEL REFINEMENT REFMAC 5.8
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 139655