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Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.451 r_long_range_B_refined 28.252 r_long_range_B_other 28.252 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 16.707 r_dihedral_angle_4_deg 14.781 r_mcangle_it 10.573 r_mcangle_other 10.573 r_scangle_other 8.979 r_mcbond_it 5.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.451 r_long_range_B_refined 28.252 r_long_range_B_other 28.252 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 16.707 r_dihedral_angle_4_deg 14.781 r_mcangle_it 10.573 r_mcangle_other 10.573 r_scangle_other 8.979 r_mcbond_it 5.767 r_mcbond_other 5.767 r_scbond_it 5.346 r_scbond_other 5.346 r_angle_other_deg 1.191 r_angle_refined_deg 1.034 r_chiral_restr 0.107 r_bond_refined_d 0.006 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 60S in complex with Nmd3, Lsg1, and Tif6 Sample Components 60S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 226516 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 19411 Reported Resolution (Å) 3.3 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) GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40 59.5
Imaging Experiment 1 2 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F30 FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 4000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.26 Imaging Mode BRIGHT FIELD BRIGHT FIELD Specimen Holder Model OTHER FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 27000 Calibrated Magnification 31000 Source FIELD EMISSION GUN FIELD EMISSION GUN Acceleration Voltage (kV) 300 300 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 MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 CLASSIFICATION RELION 1.4 RECONSTRUCTION RELION 1.4 CTF CORRECTION MotionCor2 08-22-10 INITIAL EULER ASSIGNMENT RELION 2.0 Open Beta FINAL EULER ASSIGNMENT RELION 2.0 Open Beta CLASSIFICATION RELION 2.0 Open Beta RECONSTRUCTION RELION 2.0 Open Beta
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION PHASE FLIPPING AND AMPLITUDE CORRECTION