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PSI-LHCI of the red alga Galdieria sulphuraria NIES-3638
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.837 r_dihedral_angle_2_deg 13.377 r_long_range_B_refined 9.312 r_long_range_B_other 9.312 r_scangle_other 6.522 r_dihedral_angle_1_deg 5.583 r_mcangle_it 5.097 r_mcangle_other 5.097 r_scbond_it 3.89 r_scbond_other 3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.837 r_dihedral_angle_2_deg 13.377 r_long_range_B_refined 9.312 r_long_range_B_other 9.312 r_scangle_other 6.522 r_dihedral_angle_1_deg 5.583 r_mcangle_it 5.097 r_mcangle_other 5.097 r_scbond_it 3.89 r_scbond_other 3.89 r_mcbond_it 3.115 r_mcbond_other 3.115 r_angle_refined_deg 1.808 r_angle_other_deg 0.796 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 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
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 110313 Reported Resolution (Å) 2.19 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT Servalcat 0.4.32 MODEL REFINEMENT REFMAC 5.8.0419 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2583694