5T6R

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.419
r_dihedral_angle_1_deg19.29
r_dihedral_angle_3_deg16.398
r_dihedral_angle_4_deg12.701
r_long_range_B_refined11.862
r_long_range_B_other11.862
r_mcangle_it4.295
r_mcangle_other4.295
r_scangle_other3.111
r_mcbond_it2.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.419
r_dihedral_angle_1_deg19.29
r_dihedral_angle_3_deg16.398
r_dihedral_angle_4_deg12.701
r_long_range_B_refined11.862
r_long_range_B_other11.862
r_mcangle_it4.295
r_mcangle_other4.295
r_scangle_other3.111
r_mcbond_it2.278
r_mcbond_other2.278
r_scbond_it1.768
r_scbond_other1.768
r_angle_other_deg1.178
r_angle_refined_deg0.91
r_chiral_restr0.1
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles65650
Reported Resolution (Å)4.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F30
Minimum Defocus (nm)1500
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.26
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification27000
Calibrated Magnification31000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
IMAGE ACQUISITIONLeginon
CTF CORRECTIONCTFFIND34.0.18
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION