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Rounds of 2D classification were used to select the particles that contributed to the best resolved classes. The chosen 249,600 particles were used to reconstruct an ab Initio model using D18 symmetry inferred from the 2D classes (C1 did not produce shell-like models). Homogeneous refinement using this volume as input and maintaining the symmetry yielded an interpretable model at 3.85 A resolution. To assess possible heterogeneities, a 3D classification job was run (C1 symmetry, 10 classes), but no other shell configurations could be observed. A non-uniform refinement with applied D18 symmetry of the 237,960 particles from the largest class yielded the final 3.44 A resolution map."],"id":["1"],"image_recording_id":["1"]},"em_image_recording":{"average_exposure_time":[null],"avg_electron_dose_per_subtomogram":[null],"avg_electron_dose_per_image":[44.89],"details":["Data were acquired using a Titan Krios G3i cryo-electron microscope, 300 kV (Thermo Fisher Scientific), at the LNNano facility, CNPEM, Campinas, Brazil. The microscope was equipped with a 4k-4k CMOS camera, phase plate, spherical aberration corrector, and Falcon 3 detector without energy filter or a K3 detector with energy filter. For the native YfdQ dataset, data collection utilized the Falcon 3 detector in counting mode."],"detector_mode":["COUNTING"],"film_or_detector_model":["FEI FALCON III (4k x 4k)"],"id":["1"],"imaging_id":["1"],"num_diffraction_images":[null],"num_grids_imaged":[null],"num_real_images":[null]},"em_software":{"category":["PARTICLE SELECTION","IMAGE ACQUISITION","MASKING","CTF CORRECTION","LAYERLINE INDEXING","DIFFRACTION INDEXING","MODEL FITTING","OTHER","MODEL REFINEMENT","INITIAL EULER ASSIGNMENT","FINAL EULER ASSIGNMENT","CLASSIFICATION","RECONSTRUCTION","VOLUME SELECTION","SERIES ALIGNMENT","MOLECULAR REPLACEMENT","LATTICE DISTORTION CORRECTION","SYMMETRY DETERMINATION","CRYSTALLOGRAPHY MERGING"],"details":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"id":["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19"],"image_processing_id":["1",null,null,"1",null,null,null,null,null,"1","1","1","1","1","1","1","1","1","1"],"fitting_id":[null,null,null,null,null,null,"1",null,"1",null,null,null,null,"1","1","1","1","1","1"],"imaging_id":[null,"1",null,null,null,null,null,null,null,null,null,null,null,"1","1","1","1","1","1"],"name":[null,"EPU",null,"cryoSPARC",null,null,"UCSF ChimeraX",null,"Coot",null,null,null,null,null,null,null,null,null,null],"version":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"reference_DOI":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"em_specimen":{"concentration":[null],"details":["native particles produced during phiXacm4-11 infection"],"embedding_applied":[false],"experiment_id":["1"],"id":["1"],"shadowing_applied":[false],"staining_applied":[false],"vitrification_applied":[true]},"em_virus_natural_host":{"entity_assembly_id":["1"],"id":["1"],"ncbi_tax_id":[190486],"organism":["Xanthomonas citri pv. citri str. 306"],"strain":["306"]},"pdbx_audit_support":{"funding_organization":["Sao Paulo Research Foundation (FAPESP)","Sao Paulo Research Foundation (FAPESP)","Sao Paulo Research Foundation (FAPESP)","Sao Paulo Research Foundation (FAPESP)"],"country":["Brazil","Brazil","Brazil","Brazil"],"grant_number":["2017/15340-2","2022/08730-7","2017/17303-7, 2021/10577-0","2023/13894-1, 2023/16089-2"],"ordinal":[1,2,3,4]},"atom_sites":{"entry_id":["9O7M"],"Cartn_transf_matrix[1][1]":[null],"Cartn_transf_matrix[1][2]":[null],"Cartn_transf_matrix[1][3]":[null],"Cartn_transf_matrix[2][1]":[null],"Cartn_transf_matrix[2][2]":[null],"Cartn_transf_matrix[2][3]":[null],"Cartn_transf_matrix[3][1]":[null],"Cartn_transf_matrix[3][2]":[null],"Cartn_transf_matrix[3][3]":[null],"Cartn_transf_vector[1]":[null],"Cartn_transf_vector[2]":[null],"Cartn_transf_vector[3]":[null],"Cartn_transform_axes":[null],"fract_transf_matrix[1][1]":[1],"fract_transf_matrix[1][2]":[0],"fract_transf_matrix[1][3]":[0],"fract_transf_matrix[2][1]":[0],"fract_transf_matrix[2][2]":[1],"fract_transf_matrix[2][3]":[0],"fract_transf_matrix[3][1]":[0],"fract_transf_matrix[3][2]":[0],"fract_transf_matrix[3][3]":[1],"fract_transf_vector[1]":[0],"fract_transf_vector[2]":[0],"fract_transf_vector[3]":[0],"solution_primary":[null],"solution_secondary":[null],"solution_hydrogens":[null],"special_details":[null]},"atom_type":{"symbol":["C","N","O","S"]}}}