{"EMPIAR-13091":{"imagesets":[{"segmentations":[],"name":"Unaligned multi-frame micrographs of E. coli Sig54 RNA polymerase on dhsU promoter with bEBP and ATP (Es54dhsUC1+ATP)","directory":"data/rawdata/tiffs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":17199,"frames_per_image":35,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.43,"pixel_height":0.43,"micrographs_file_pattern":"data/rawdata/tiffs/AM38-1_*.tif","picked_particles_file_pattern":"data/particle_stacks/*.star","picked_particles_directory":"data/shiny_particles/job007/tiffs","details":"Raw micrographs were collected on a Titan Krios at 300kV with Cs correction and an energy filter slit width of 20eV on Gatan K3 camera in super-resolution mode. Recordings were performed at a pixel size of 0.86 A/px (at the camera; images in super-resolution 0.43 A/px) with a dose rate of 22 electrons/px/s for an exposure time of 1.4 seconds in dose-fraction mode of 40 milliseconds per-frame resulting in a total of 35 frames and a total dose of 42 electrons/A^2. Defocus range for the collection was -0.8 to -2.2 microns.","image_width":"11520","image_height":"8184"},{"segmentations":[],"name":"Aligned single-frame micrographs of E. coli Sig54 RNA polymerase on dhsU promoter with bEBP and ATP (Es54dhsUC1+ATP)","directory":"data/motion_corrected/job002/tiffs","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":17199,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.86,"pixel_height":0.86,"micrographs_file_pattern":"data/motion_corrected/job002/tiffs/AM38-1_*.mrc","picked_particles_file_pattern":"data/particle_stacks/*.star","picked_particles_directory":"data/shiny_particles/job007/tiffs","details":"Raw micrograph frames were aligned using MotionCor2 (through Relion) with a binning factor of 2 and a dose of 1.189 electrons/A^2/frame. Additional files from the job output are provided in the upstream directory.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Individual per-particle motion-corrected particle images of E. coli Sig54 RNA polymerase on dhsU promoter with bEBP and ATP (Es54dhsUC1+ATP)","directory":"data/shiny_particles/job007/tiffs","category":"picked particles - single frame - processed","header_format":"MRCS","data_format":"MRCS","num_images_or_tilt_series":16461,"frames_per_image":0,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.86,"pixel_height":0.86,"micrographs_file_pattern":"data/shiny_particles/job007/tiffs/AM38-1_*_shiny.mrcs","picked_particles_file_pattern":"data/particle_stacks/*.star","picked_particles_directory":"data/shiny_particles/job007/tiffs","details":"Frames per image are different in each mrcs file as the frames represent the number of particles used from each corresponding micrograph (frames = 0 was used as placeholder). Reference-base per-particle motion-correction was performed using Relion Bayesian Polishing. Additional files from the job output are provided in the upstream directory. Particle stacks for each final class of the data processing and the consensus reconstruction are provided as STAR files (converted from cryoSPARC using pyem v0.67 as follows: csparc2star.py --inverty particles.cs passthrough.cs).","image_width":"448","image_height":"448"}],"workflow_file":null,"grant_references":[{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R35 GM118130","country":"United States"}],"version_history":[],"title":"CryoEM of E. coli RNA polymerase Sigma N transcription initiation intermediates","principal_investigator":[{"author_orcid":"0000-0002-8241-3153","middle_name":null,"organization":"The Rockefeller University","street":"1230 York Avenue","town_or_city":"New York","state_or_province":"New York","post_or_zip":"10065","telephone":null,"fax":null,"first_name":"Seth","last_name":"Darst","email":"darst [at] rockefeller.edu","country":"United States","entry":"EMPIAR-13091"}],"status":"REL","deposition_date":"2025-01-14","release_date":"2025-12-06","obsolete_date":null,"update_date":"2025-12-06","corresponding_author":{"author":{"author_orcid":"0000-0002-8241-3153","middle_name":null,"organization":"The Rockefeller University","street":"1230 York Avenue","town_or_city":"New York","state_or_province":"New York","post_or_zip":"10065","first_name":"Seth","last_name":"Darst","country":"United States"}},"authors":[{"author":{"name":"Mueller AU","author_orcid":"0000-0003-3002-3695"}},{"author":{"name":"Molina N","author_orcid":"0009-0007-9006-214X"}},{"author":{"name":"Nixon BT","author_orcid":null}},{"author":{"name":"Darst SA","author_orcid":"0000-0002-8241-3153"}}],"cross_references":["EMD-48589","EMD-48586","EMD-48588","EMD-48590","EMD-48587"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Mueller AU","author_orcid":"0000-0003-3002-3695"},{"name":"Molina N","author_orcid":"0009-0007-9006-214X"},{"name":"Nixon BT","author_orcid":null},{"name":"Darst SA","author_orcid":"0000-0002-8241-3153"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding","volume":"16","country":"","first_page":null,"last_page":null,"year":"2025","language":"English","doi":"10.1038/s41467-025-61837-4","pubmedid":"40759887","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature communications","journal_abbreviation":"Nat Commun","issue":"1","preprint":false}],"dataset_size":"10.5 TB","experiment_type":"EMDB","scale":"molecule","related_pdb_entries":["9msh","9mse","9msg","9msj","9msf"],"entry_doi":"10.6019/EMPIAR-13091"}}