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Cryo-EM structure of the channelrhodopsin GtCCR2
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
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
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