{"EMPIAR-11827":{"imagesets":[{"segmentations":[],"name":"Extracted particles and orientations for final reconstruction of SARS-CoV-2 5' stem-loop 5 RNA.","directory":"data/SARS-CoV-2_SL5/particles","category":"picked particles - single frame - processed","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":445981,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"","picked_particles_file_pattern":"data/SARS-CoV-2_SL5/particles/data/*mrc","picked_particles_directory":"data/SARS-CoV-2_SL5/particles/data","details":"Particles extracted from motion-corrected micrographs. The orientations for the final reconstruction can be found in data/SARS-CoV-2_SL5/particles/P1_J791_particles_exported.cs.","image_width":"360","image_height":"360"},{"segmentations":[],"name":"Unaligned multi-frame micrographs of SARS-CoV-2 5' stem-loops 5 RNA dataset 1.","directory":"data/SARS-CoV-2_SL5/exposures1","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":12633,"frames_per_image":40,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"data/SARS-CoV-2_SL5/exposures1/GridSquare_*/FoilHole_*_Fractions.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector. Over the collection, the sample was exposed evenly to 50 electrons per angstrom squared with a total exposure time of 6.00 seconds. Desired defocuses ranged from -1.2 to -2.5 nm. The exposures are gain corrected.","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Unaligned multi-frame micrographs of SARS-CoV-2 5' stem-loops 5 RNA dataset 2.","directory":"data/SARS-CoV-2_SL5/exposures2","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4217,"frames_per_image":40,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"data/SARS-CoV-2_SL5/exposures2/GridSquare_*/FoilHole_*_Fractions.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector. Over the collection, the sample was exposed evenly to 50 electrons per angstrom squared with a total exposure time of 3.84 seconds. Desired defocuses ranged from -1.2 to -2.2 nm. The exposures are gain corrected.\n\n4.13\t5.56\n-1.0 to -2.0\t-1.0 to -2.0\n4,592\t5,540","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Unaligned multi-frame micrographs of SARS-CoV-2 5' stem-loops 5 RNA dataset 3.","directory":"data/SARS-CoV-2_SL5/exposures3","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4592,"frames_per_image":40,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"data/SARS-CoV-2_SL5/exposures3/GridSquare_*/FoilHole_*_Fractions.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector. Over the collection, the sample was exposed evenly to 50 electrons per angstrom squared with a total exposure time of 4.13 seconds. Desired defocuses ranged from -1.0 to -2.0 nm. The exposures are gain corrected.\n\n4.13\t5.56\n-1.0 to -2.0\n5,540","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Unaligned multi-frame micrographs of SARS-CoV-2 5' stem-loops 5 RNA dataset 4.","directory":"data/SARS-CoV-2_SL5/exposures4","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":5540,"frames_per_image":40,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"data/SARS-CoV-2_SL5/exposures4/GridSquare_*/FoilHole_*_Fractions.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector. Over the collection, the sample was exposed evenly to 50 electrons per angstrom squared with a total exposure time of 5.56 seconds. Desired defocuses ranged from -1.0 to -2.0 nm. The exposures are gain corrected.","image_width":"4096","image_height":"4096"}],"workflow_file":null,"grant_references":[{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R35GM122579","country":"United States"},{"funding_body":"Howard Hughes Medical Institute (HHMI)","code":"N/A","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"U24GM129541","country":"United States"},{"funding_body":"National Science Foundation (NSF, United States)","code":"GRFPDGE1656518","country":"United States"}],"version_history":[],"title":"Cryo-EM of SARS-CoV-2 5' proximal stem-loop 5","principal_investigator":[{"author_orcid":"0000-0002-8910-3078","middle_name":null,"organization":"Department of Bioengineering, James H. Clark Center, Stanford University; CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory","street":"318 CAMPUS DR","town_or_city":"Stanford","state_or_province":"CA","post_or_zip":"94305","telephone":null,"fax":null,"first_name":"Wah","last_name":"Chiu","email":"wahc [at] stanford.edu","country":"United States","entry":"EMPIAR-11827"}],"status":"REL","deposition_date":"2023-11-28","release_date":"2025-07-12","obsolete_date":null,"update_date":"2025-07-12","corresponding_author":{"author":{"author_orcid":"0000-0001-7497-0972","middle_name":null,"organization":"Department of Biochemistry, Stanford University; Howard Hughes Medical Institute","street":"279 Campus Dr W","town_or_city":"Stanford","state_or_province":"CA","post_or_zip":"94305","first_name":"Rhiju","last_name":"Das","country":"United States"}},"authors":[{"author":{"name":"Kretsch RC","author_orcid":"0000-0002-6935-518X"}},{"author":{"name":"Xu L","author_orcid":"0000-0002-1200-8937"}},{"author":{"name":"Zheludev IN","author_orcid":"0000-0002-9572-0574"}},{"author":{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"}},{"author":{"name":"Huang R","author_orcid":"0009-0009-6136-8013"}},{"author":{"name":"Nye G","author_orcid":"0009-0001-6698-9988"}},{"author":{"name":"Li S","author_orcid":"0000-0002-7041-5960"}},{"author":{"name":"Zhang K","author_orcid":"0000-0003-0414-4776"}},{"author":{"name":"Chiu W","author_orcid":"0000-0002-8910-3078"}},{"author":{"name":"Das R","author_orcid":"0000-0001-7497-0972"}}],"cross_references":["EMD-42818"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Kretsch RC","author_orcid":"0000-0002-6935-518X"},{"name":"Xu L","author_orcid":"0000-0002-1200-8937"},{"name":"Zheludev IN","author_orcid":null},{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"},{"name":"Huang R","author_orcid":null},{"name":"Nye G","author_orcid":null},{"name":"Li S","author_orcid":null},{"name":"Zhang K","author_orcid":null},{"name":"Chiu W","author_orcid":"0000-0002-8910-3078"},{"name":"Das R","author_orcid":"0000-0001-7497-0972"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses","volume":"121","country":"","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1073/pnas.2320493121","pubmedid":"38427602","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Proceedings of the National Academy of Sciences of the United States of America","journal_abbreviation":"Proc Natl Acad Sci U S A","issue":"10","preprint":false},{"authors":[{"name":"Kretsch RC","author_orcid":null},{"name":"Xu L","author_orcid":"0000-0002-1200-8937"},{"name":"Zheludev IN","author_orcid":"0000-0002-9572-0574"},{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"},{"name":"Huang R","author_orcid":null},{"name":"Nye G","author_orcid":null},{"name":"Li S","author_orcid":"0000-0002-7041-5960"},{"name":"Zhang K","author_orcid":null},{"name":"Chiu W","author_orcid":null},{"name":"Das R","author_orcid":"0000-0001-7497-0972"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Tertiary folds of the SL5 RNA from the 5′ proximal region of SARS-CoV-2 and related coronaviruses","volume":null,"country":"","first_page":null,"last_page":null,"year":null,"language":null,"doi":"10.1101/2023.11.22.567964","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"34.1 TB","experiment_type":"EMDB","scale":"molecule","related_pdb_entries":["8uys"],"entry_doi":"10.6019/EMPIAR-11827"}}