8YEK

Cryo-EM structure of the channelrhodopsin GtCCR2

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.893
r_dihedral_angle_3_deg	16.047
r_dihedral_angle_4_deg	11.876
r_long_range_B_refined	4.148
r_long_range_B_other	4.148
r_dihedral_angle_1_deg	3.246
r_angle_other_deg	1.535
r_mcangle_it	1.338
r_mcangle_other	1.337
r_angle_refined_deg	1.085
r_scangle_other	0.965
r_mcbond_it	0.724
r_mcbond_other	0.723
r_scbond_it	0.512
r_scbond_other	0.512
r_chiral_restr	0.061
r_bond_other_d	0.031
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
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
GtCCR2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	457536
Reported Resolution (Å)	2.73
Resolution Method	FSC 0.143 CUT-OFF
Other Details	With C3 symmetry
Refinement Type
Symmetry Type	POINT

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

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DARK FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.2
CTF CORRECTION	cryoSPARC	3.3.2
MODEL FITTING	MOLREP
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Servalcat
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		5791254