8R0N | pdb_00008r0n

Cryo-EM structure of the microbial rhodopsin CryoR1 at pH 10.5 in detergent in the ground state


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other14.501
r_long_range_B_refined14.495
r_dihedral_angle_3_deg13.273
r_scangle_other11.803
r_mcangle_it9.53
r_mcangle_other9.53
r_dihedral_angle_2_deg8.687
r_scbond_it7.249
r_scbond_other7.249
r_mcbond_it6.216
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other14.501
r_long_range_B_refined14.495
r_dihedral_angle_3_deg13.273
r_scangle_other11.803
r_mcangle_it9.53
r_mcangle_other9.53
r_dihedral_angle_2_deg8.687
r_scbond_it7.249
r_scbond_other7.249
r_mcbond_it6.216
r_mcbond_other6.216
r_dihedral_angle_1_deg5.029
r_angle_refined_deg1.301
r_angle_other_deg0.458
r_chiral_restr0.065
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 Particles200653
Reported Resolution (Å)2.7
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 ModelTFS KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2200
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)300
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