8YEL

Cryo-EM structure of the channelrhodopsin GtCCR4


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.081
r_dihedral_angle_4_deg24.024
r_dihedral_angle_3_deg18.904
r_long_range_B_refined9.148
r_long_range_B_other9.147
r_dihedral_angle_1_deg4.287
r_mcangle_it2.437
r_mcangle_other2.436
r_scangle_other1.7
r_angle_other_deg1.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.081
r_dihedral_angle_4_deg24.024
r_dihedral_angle_3_deg18.904
r_long_range_B_refined9.148
r_long_range_B_other9.147
r_dihedral_angle_1_deg4.287
r_mcangle_it2.437
r_mcangle_other2.436
r_scangle_other1.7
r_angle_other_deg1.496
r_mcbond_other1.318
r_mcbond_it1.317
r_angle_refined_deg1.133
r_scbond_it0.889
r_scbond_other0.889
r_chiral_restr0.064
r_bond_other_d0.03
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.002
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
GtCCR4
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles581115
Reported Resolution (Å)2.71
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsWith C3 symmetry
Refinement Type
Symmetry TypePOINT
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 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGMOLREP
MODEL REFINEMENTPHENIX
MODEL REFINEMENTServalcat
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION5403048