5T62 | pdb_00005t62

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.451
r_long_range_B_refined28.252
r_long_range_B_other28.252
r_dihedral_angle_3_deg16.713
r_dihedral_angle_1_deg16.707
r_dihedral_angle_4_deg14.781
r_mcangle_it10.573
r_mcangle_other10.573
r_scangle_other8.979
r_mcbond_it5.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.451
r_long_range_B_refined28.252
r_long_range_B_other28.252
r_dihedral_angle_3_deg16.713
r_dihedral_angle_1_deg16.707
r_dihedral_angle_4_deg14.781
r_mcangle_it10.573
r_mcangle_other10.573
r_scangle_other8.979
r_mcbond_it5.767
r_mcbond_other5.767
r_scbond_it5.346
r_scbond_other5.346
r_angle_other_deg1.191
r_angle_refined_deg1.034
r_chiral_restr0.107
r_bond_refined_d0.006
r_gen_planes_refined0.005
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, Lsg1, and Tif6
Sample Components
60S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles226516
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Number of Particles19411
Reported Resolution (Å)3.3
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)GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)4059.5
Imaging Experiment12
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F30FEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.26
Imaging ModeBRIGHT FIELDBRIGHT FIELD
Specimen Holder ModelOTHERFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification27000
Calibrated Magnification31000
SourceFIELD EMISSION GUNFIELD EMISSION GUN
Acceleration Voltage (kV)300300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
IMAGE ACQUISITIONLeginon
CTF CORRECTIONCTFFIND34.0.18
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTCoot
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
CTF CORRECTIONMotionCor208-22-10
INITIAL EULER ASSIGNMENTRELION2.0 Open Beta
FINAL EULER ASSIGNMENTRELION2.0 Open Beta
CLASSIFICATIONRELION2.0 Open Beta
RECONSTRUCTIONRELION2.0 Open Beta
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
PHASE FLIPPING AND AMPLITUDE CORRECTION