{"EMPIAR-11125":{"imagesets":[{"segmentations":[],"name":"Reconstructed sample tomograms of purified alpha-carboxysomes, plus frames","directory":"data/CBTomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":3,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":8.832,"pixel_height":8.832,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"SIRT-like filtered reconstructed tomograms with bin8 pixel size.  These tomograms illustrate different features of alpha-carboxysomes, noted in the accompanying citation.  Tomograms have different image heights; see MRC header for more details.  Frame stacks (gain-corrected) and mdoc files are included for users wishing to reconstruct in their own programs.","image_width":"511","image_height":"313"},{"segmentations":[],"name":"Reconstructed sample tomograms of wild-type H. neapolitanus cells, plus frames","directory":"data/HaloTomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":3,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED BYTE","pixel_width":8.612,"pixel_height":8.612,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"SIRT-reconstructed tomograms with bin4 pixel size.  These tomograms illustrate different features of alpha-carboxysomes in vivo, noted in the accompanying citation.  Tomograms have different image heights; see MRC header for more details.  Frame stacks and mdoc files are included for users wishing to reconstruct in their own programs.","image_width":"1024","image_height":"500"},{"segmentations":[],"name":"Complete set of subtomograms for Rubisco subtomogram average","directory":"data","category":"picked particles - multiframe - unprocessed","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":32930,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.104,"pixel_height":1.104,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"subtomograms.tar.gz contains the complete set of Rubisco subtomograms from the purified alpha-carboxysome dataset. The file pattern is subtomograms/particle_*.mrc, and the picked particles file is subtomograms/particles.csv. Subtomograms were cropped in Dynamo from from bin1 WBP tomograms reconstructed in novaCTF. The particles.csv text file contains position and orientation information for each subtomogram, as well as defocus, carboxysome number, cross-correlation coefficient, and other data to allow users to import subtomograms into the software package of their choice. A detailed description of the csv information is in the csvColumnDefinitions.txt file, also in the subtomograms directory.","image_width":"160","image_height":"160"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Cryo electron tomography of H. neapolitanus alpha-carboxysomes","principal_investigator":[{"author_orcid":"0000-0003-1556-4864","middle_name":"J","organization":"College of Physical and Mathematical Sciences, Brigham Young University","street":"N-181 H ESC","town_or_city":"Provo","state_or_province":"UT","post_or_zip":"84602","telephone":"801-422-7413","fax":null,"first_name":"Grant","last_name":"Jensen","email":"grant_jensen [at] byu.edu","country":"United States","entry":"EMPIAR-11125"},{"author_orcid":"0000-0002-8073-6960","middle_name":null,"organization":"Departments of Biological Sciences and Chemistry, College of Science, Purdue University","street":"Hockmeyer Hall Room 231, 240 S Martin Jischke Dr","town_or_city":"West Lafayette","state_or_province":"IN","post_or_zip":"47907","telephone":"+1 765 494 4909","fax":null,"first_name":"Lauren Ann","last_name":"Metskas","email":"metskas [at] purdue.edu","country":"United States","entry":"EMPIAR-11125"},{"author_orcid":"0000-0003-0042-2257","middle_name":"F","organization":"Dept of Molecular & Cell Biology, University of California Berkeley","street":"142 Weill Hall #3200","town_or_city":"Berkeley","state_or_province":"CA","post_or_zip":"94720","telephone":"(510) 643-7847","fax":null,"first_name":"David","last_name":"Savage","email":"savage [at] berkeley.edu","country":"United States","entry":"EMPIAR-11125"}],"status":"REL","deposition_date":"2022-07-18","release_date":"2022-08-12","obsolete_date":null,"update_date":"2022-09-05","corresponding_author":{"author":{"author_orcid":"0000-0003-1556-4864","middle_name":"J","organization":"College of Physical and Mathematical Sciences, Brigham Young University","street":"N-181 H ESC","town_or_city":"Provo","state_or_province":"UT","post_or_zip":"84602","first_name":"Grant","last_name":"Jensen","country":"United States"}},"authors":[{"author":{"name":"Metskas LA","author_orcid":"0000-0002-8073-6960"}},{"author":{"name":"Ortega D","author_orcid":"0000-0002-8344-2335"}},{"author":{"name":"Oltrogge LM","author_orcid":"0000-0001-5716-9980"}},{"author":{"name":"Blikstad C","author_orcid":"0000-0001-5740-926X"}},{"author":{"name":"Laughlin T","author_orcid":"0000-0001-8943-1330"}},{"author":{"name":"Savage DF","author_orcid":"0000-0003-0042-2257"}},{"author":{"name":"Jensen GJ","author_orcid":"0000-0003-1556-4864"}}],"cross_references":["EMD-27654"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Metskas LA","author_orcid":"0000-0002-8073-6960"},{"name":"Ortega D","author_orcid":"0000-0002-8344-2335"},{"name":"Oltrogge LM","author_orcid":"0000-0001-5716-9980"},{"name":"Blikstad C","author_orcid":"0000-0001-5740-926X"},{"name":"Laughlin T","author_orcid":"0000-0001-8943-1330"},{"name":"Savage DF","author_orcid":"0000-0003-0042-2257"},{"name":"Jensen GJ","author_orcid":"0000-0003-1556-4864"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Rubisco forms a lattice inside alpha-carboxysomes","volume":null,"country":"","first_page":null,"last_page":null,"year":"2022","language":null,"doi":"10.1101/2022.01.24.477598","pubmedid":null,"details":"This deposition includes: 3 example tomograms with movie frames of purified H. neapolitanus carboxysomes, 3 example tomograms with movie frames of H. neapolitanus cells, associated mdoc files for the tomograms, and the complete set of subtomograms for the Rubisco subtomogram average in EMD-27654.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true},{"authors":[{"name":"Metskas LA","author_orcid":"0000-0002-8073-6960"},{"name":"Ortega D","author_orcid":null},{"name":"Oltrogge LM","author_orcid":"0000-0001-5716-9980"},{"name":"Blikstad C","author_orcid":"0000-0001-5740-926X"},{"name":"Lovejoy DR","author_orcid":null},{"name":"Laughlin TG","author_orcid":"0000-0001-8943-1330"},{"name":"Savage DF","author_orcid":"0000-0003-0042-2257"},{"name":"Jensen GJ","author_orcid":"0000-0003-1556-4864"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Rubisco forms a lattice inside alpha-carboxysomes","volume":"13","country":"","first_page":null,"last_page":null,"year":"2022","language":"English","doi":"10.1038/s41467-022-32584-7","pubmedid":"35982043","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature communications","journal_abbreviation":"Nat Commun","issue":"1","preprint":false}],"dataset_size":"483.4 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-11125"}}