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Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.419 r_dihedral_angle_1_deg 19.29 r_dihedral_angle_3_deg 16.398 r_dihedral_angle_4_deg 12.701 r_long_range_B_refined 11.862 r_long_range_B_other 11.862 r_mcangle_it 4.295 r_mcangle_other 4.295 r_scangle_other 3.111 r_mcbond_it 2.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.419 r_dihedral_angle_1_deg 19.29 r_dihedral_angle_3_deg 16.398 r_dihedral_angle_4_deg 12.701 r_long_range_B_refined 11.862 r_long_range_B_other 11.862 r_mcangle_it 4.295 r_mcangle_other 4.295 r_scangle_other 3.111 r_mcbond_it 2.278 r_mcbond_other 2.278 r_scbond_it 1.768 r_scbond_other 1.768 r_angle_other_deg 1.178 r_angle_refined_deg 0.91 r_chiral_restr 0.1 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 60S in complex with Nmd3
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 65650 Reported Resolution (Å) 4.2 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 Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F30 Minimum Defocus (nm) 1500 Maximum Defocus (nm) 4000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.26 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 27000 Calibrated Magnification 31000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 1.4 IMAGE ACQUISITION Leginon CTF CORRECTION CTFFIND3 4.0.18 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 CLASSIFICATION RELION 1.4 RECONSTRUCTION RELION 1.4 MODEL REFINEMENT Coot
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION