8RQ5

Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.413
r_long_range_B_refined10.211
r_long_range_B_other10.211
r_scangle_other8.715
r_dihedral_angle_2_deg8.53
r_mcangle_it5.686
r_mcangle_other5.686
r_scbond_it5.644
r_scbond_other5.644
r_dihedral_angle_1_deg5.028
Sample
Sodium-pumping rhodopsin
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification DetailsJet vitrified with EasyGrid
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles333078
Reported Resolution (Å)2.32
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)40.3
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.2
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.2
INITIAL EULER ASSIGNMENTcryoSPARC4.2
FINAL EULER ASSIGNMENTcryoSPARC4.2
CLASSIFICATIONcryoSPARC4.2
RECONSTRUCTIONcryoSPARC4.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1916000A first round of blob picking was performed and used to obtain an initial model. this initial model was used to generate templates that were then used to performed template picking, resulting in 1916000 particles