{"EMPIAR-12002":{"imagesets":[{"segmentations":[],"name":"Unaligned multi-frame micrographs of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - \"Elizabeth\"","directory":"data/rawdata","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":23259,"frames_per_image":40,"frame_range_min":1,"frame_range_max":40,"voxel_type":"UNSIGNED BYTE","pixel_width":0.646,"pixel_height":0.646,"micrographs_file_pattern":"data/rawdata/n21sep13b*enn.frames.tif","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The dataset contains unaligned non gain-corrected micrograph movies in TIFF format. Cryo-EM data were collected at the National Center for Cryo-EM Access and Training (NCCAT) using the 300kV Titan Krios #4 – “Elizabeth” (TFS) electron microscope, equipped with a K3 direct electron detector (Gatan) and a BioQuantum energy filter (Gatan) with slit width of 20 eV. Data were collected automatically in counting mode using image shift in Leginon, a nominal magnification of 130,000X, a nominal pixel size of 0.646 Å/pixel, and a dose rate of 19.9685 electrons/pixel/s. Movies were recorded at 30 ms/frame for 1.2s (40 frames total), resulting in a total dose of 57.42 electrons/Å2. Nominal defocus range was -0.8 to -2.0 μm. A total of 23,259 micrographs were recorded from one grid over three days. Micrographs were not gain-normalized or defect corrected. The gain reference is the file named \"n21sep13b*norm_0.mrc\" in the \"references\" folder. When importing into cryoSPARC the gain reference should be flipped in the Y axis. At the end of processing a calibrated pixel size of 0.67 Å/pixel was determined for this dataset, representing an 3.72% error from the nominal pixel size value.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Aligned and dose-weighted micrographs of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - \"Elizabeth\"","directory":"data/aligned","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":16451,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.646,"pixel_height":0.646,"micrographs_file_pattern":"data/aligned/*patch_aligned_doseweighted.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Aligned and dose-weighted micrographs produced from the raw movies using patch motion correction in cryoSPARC. The dataset contains a subset of micrographs that have contributed particles to the final particle stack. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Final particle stack of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - \"Elizabeth\"","directory":"data/particles","category":"picked particles - single frame - processed","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":16451,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.646,"pixel_height":0.646,"micrographs_file_pattern":"data/particles/extract/*patch_aligned_doseweighted_particles.mrc","picked_particles_file_pattern":"data/particles/J253_particles_exported.cs","picked_particles_directory":"","details":"Final particle stack of 490,807 particles from 16,451 aligned/dose-weighted micrographs corresponding to the reconstruction deposited in EMD-44302. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel. Box size of 480 px was used.","image_width":"480","image_height":"480"}],"workflow_file":null,"grant_references":[{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R00GM123228","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R35GM150831","country":"United States"}],"version_history":[],"title":"Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Krios microscope","principal_investigator":[{"author_orcid":"0000-0002-3194-9863","middle_name":"I","organization":"Rutgers New Jersey Medical School","street":"225 Warren Street","town_or_city":"Newark","state_or_province":"NJ","post_or_zip":"07103","telephone":"+1 973 972 4498","fax":null,"first_name":"Vasileios","last_name":"Petrou","email":"vasileios.petrou [at] rutgers.edu","country":"United States","entry":"EMPIAR-12002"}],"status":"REL","deposition_date":"2024-03-05","release_date":"2025-06-02","obsolete_date":null,"update_date":"2025-06-02","corresponding_author":{"author":{"author_orcid":"0000-0002-3194-9863","middle_name":"I","organization":"Rutgers New Jersey Medical School","street":"225 Warren Street","town_or_city":"Newark","state_or_province":"NJ","post_or_zip":"07103","first_name":"Vasileios","last_name":"Petrou","country":"United States"}},"authors":[{"author":{"name":"Ashraf KU","author_orcid":"0000-0002-0799-4947"}},{"author":{"name":"Punetha A","author_orcid":"0000-0002-2845-5459"}},{"author":{"name":"Kaelber JT","author_orcid":"0000-0001-9426-1030"}},{"author":{"name":"Petrou VI","author_orcid":"0000-0002-3194-9863"}}],"cross_references":["EMD-44302"],"biostudies_references":[],"idr_references":[],"empiar_references":[{"name":"EMPIAR-11924"}],"citation":[{"authors":[{"name":"Ashraf KU","author_orcid":"0000-0002-0799-4947"},{"name":"Bunoro-Batista M","author_orcid":"0000-0002-2468-748X"},{"name":"Ansell TB","author_orcid":null},{"name":"Punetha A","author_orcid":"0000-0002-2845-5459"},{"name":"Rosario-Garrido S","author_orcid":"0009-0006-3350-6448"},{"name":"Firlar E","author_orcid":"0000-0003-0190-6528"},{"name":"Kaelber JT","author_orcid":"0000-0001-9426-1030"},{"name":"Stansfeld PJ","author_orcid":"0000-0001-8800-7669"},{"name":"Petrou VI","author_orcid":"0000-0002-3194-9863"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria","volume":null,"country":"United States","first_page":null,"last_page":null,"year":"2025","language":"English","doi":"10.1101/2025.01.29.634835","pubmedid":null,"details":"The single-particle cryo-EM dataset contains unaligned movies (40 frames per movie, accumulated exposure of 57.42 electrons per angstrom squared, non-gain corrected, gain reference provided), patch-aligned/doseweighted micrographs (subset contributing to final particle stack) and final particle stack used for reconstruction deposited in EMD-44302.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"bioRxiv","issue":null,"preprint":true}],"dataset_size":"5.9 TB","experiment_type":"EMDB","scale":"molecule","related_pdb_entries":["9b77"],"entry_doi":"10.6019/EMPIAR-12002"}}