8QQZ

Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form at pH 8.0


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.914
r_long_range_B_refined9.285
r_long_range_B_other9.284
r_dihedral_angle_2_deg9.075
r_scangle_other7.69
r_dihedral_angle_1_deg5.288
r_scbond_it4.624
r_scbond_other4.624
r_mcangle_it4.384
r_mcangle_other4.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.914
r_long_range_B_refined9.285
r_long_range_B_other9.284
r_dihedral_angle_2_deg9.075
r_scangle_other7.69
r_dihedral_angle_1_deg5.288
r_scbond_it4.624
r_scbond_other4.624
r_mcangle_it4.384
r_mcangle_other4.384
r_mcbond_it2.923
r_mcbond_other2.906
r_angle_refined_deg1.48
r_angle_other_deg0.51
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d
r_dihedral_angle_4_deg
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
Light-driven sodium pump ErNaR
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles437017
Reported Resolution (Å)2.63
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeOTHER
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.0.2
CTF CORRECTIONcryoSPARC4.0.2
INITIAL EULER ASSIGNMENTcryoSPARC4.0.2
FINAL EULER ASSIGNMENTcryoSPARC4.0.2
CLASSIFICATIONcryoSPARC4.0.2
RECONSTRUCTIONcryoSPARC4.0.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION