8R0M | pdb_00008r0m

Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 8.0 in detergent


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.761
r_long_range_B_refined12.168
r_long_range_B_other12.168
r_scangle_other9.682
r_dihedral_angle_2_deg7.472
r_mcangle_it6.961
r_mcangle_other6.96
r_dihedral_angle_1_deg5.964
r_scbond_it5.745
r_scbond_other5.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.761
r_long_range_B_refined12.168
r_long_range_B_other12.168
r_scangle_other9.682
r_dihedral_angle_2_deg7.472
r_mcangle_it6.961
r_mcangle_other6.96
r_dihedral_angle_1_deg5.964
r_scbond_it5.745
r_scbond_other5.745
r_mcbond_it4.296
r_mcbond_other4.295
r_angle_refined_deg1.592
r_angle_other_deg0.523
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.007
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
Pentameric form of the microbial rhodopsin CryoR1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles333882
Reported Resolution (Å)2.87
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 K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)53.1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
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 Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.1.2
CTF CORRECTIONcryoSPARC4.1.2
INITIAL EULER ASSIGNMENTcryoSPARC4.1.2
FINAL EULER ASSIGNMENTcryoSPARC4.1.2
CLASSIFICATIONcryoSPARC4.1.2
RECONSTRUCTIONcryoSPARC4.1.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION