8R0M | pdb_00008r0m

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

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.761
r_long_range_B_refined	12.168
r_long_range_B_other	12.168
r_scangle_other	9.682
r_dihedral_angle_2_deg	7.472
r_mcangle_it	6.961
r_mcangle_other	6.96
r_dihedral_angle_1_deg	5.964
r_scbond_it	5.745
r_scbond_other	5.745
r_mcbond_it	4.296
r_mcbond_other	4.295
r_angle_refined_deg	1.592
r_angle_other_deg	0.523
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
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 State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	333882
Reported Resolution (Å)	2.87
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	53.1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	OTHER
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.1.2
CTF CORRECTION	cryoSPARC	4.1.2
INITIAL EULER ASSIGNMENT	cryoSPARC	4.1.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.1.2
CLASSIFICATION	cryoSPARC	4.1.2
RECONSTRUCTION	cryoSPARC	4.1.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION