{"EMPIAR-10307":{"imagesets":[{"segmentations":[],"name":"Dataset 1 of human pre-B spliceosome; motion-corrected micrographs","directory":"data/MotionCorr/job007","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4627,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.025,"pixel_height":1.025,"micrographs_file_pattern":"data/MotionCorr/job007/Raw_data/FoilHole_*_Data_*_*_201810*_*-*.mrc","picked_particles_file_pattern":"data/dataset1_CRYOLOpicking.star","picked_particles_directory":"data","details":"Micrographs were averaged using RELION 3.0 implementation of MotionCor2 with 5x5 patches and dose-weighting. Original movies were 40 frames with a total dose of 57 electrons per squared Angstrom over 8 seconds.\nData collected on Titan Krios 2 at the Astbury Biostructure Laboratory, University of Leeds, on a K2 detector operated in counting mode.\ndataset1_CRYOLOpicking.star contains particle coordinates picked by CRYOLO (X and Y in 1st and 2nd columns; remainder of .star file is output of RELION particle extraction job, extracted particles not deposited here)","image_width":"3838","image_height":"3710"},{"segmentations":[],"name":"Dataset 2 of human pre-B spliceosome; motion-corrected micrographs","directory":"data/MotionCorr/job593","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":6869,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.022,"pixel_height":1.022,"micrographs_file_pattern":"data/MotionCorr/job593/Movies_2Nov/FoilHole_*_Data_*_*_201811*_*-*.mrc","picked_particles_file_pattern":"data/dataset2_CRYOLOpicking.star","picked_particles_directory":"data","details":"Micrographs were averaged using RELION 3.0 implementation of MotionCor2 with 5x5 patches and dose-weighting. Original movies were 40 frames with a total dose of 50 electrons per squared Angstrom over 6 seconds.\nData collected on Titan Krios 3 at the MRC Laboratory of Molecular Biology on a K2 detector operated in counting mode.\ndataset2_CRYOLOpicking.star contains particle coordinates picked by CRYOLO (X and Y in 1st and 2nd columns; remainder of .star file is output of RELION particle extraction job, extracted particles not deposited here)","image_width":"3838","image_height":"3710"},{"segmentations":[],"name":"Dataset 3 of human pre-B spliceosome; motion-corrected micrographs","directory":"data/MotionCorr/job843/Movies_20Dec","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":7303,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.02,"pixel_height":1.02,"micrographs_file_pattern":"data/MotionCorr/job843/Movies_20Dec/FoilHole_*_Data_*_*_201812*_*-*.mrc","picked_particles_file_pattern":"data/dataset3_CRYOLOpicking.star","picked_particles_directory":"data","details":"Micrographs were averaged using RELION 3.0 implementation of MotionCor2 with 5x5 patches and dose-weighting. Original movies were 40 frames with a total dose of 55.4 electrons per squared Angstrom over 12 seconds.\nData collected on a Titan Krios at the University of Cambridge biochemistry department on a K2 detector operated in counting mode.\ndataset3_CRYOLOpicking.star contains particle coordinates picked by CRYOLO (X and Y in 1st and 2nd columns; remainder of .star file is output of RELION particle extraction job, extracted particles not deposited here)","image_width":"3838","image_height":"3710"},{"segmentations":[],"name":"Dataset 4 of human pre-B spliceosome; motion-corrected micrographs","directory":"data/MotionCorr/job890/Movies_11Jan","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":6672,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.022,"pixel_height":1.022,"micrographs_file_pattern":"data/MotionCorr/job890/Movies_11Jan/FoilHole_*_Data_*_*_201901*_*-*.mrc","picked_particles_file_pattern":"data/dataset4_CRYOLOpicking.star","picked_particles_directory":"data","details":"Micrographs were averaged using RELION 3.0 implementation of MotionCor2 with 5x5 patches and dose-weighting. Original movies were 40 frames with a total dose of 48.6 electrons per squared Angstrom over 6 seconds.\nData collected on Titan Krios 3 at the MRC Laboratory of Molecular Biology on a K2 detector operated in counting mode.\ndataset4_CRYOLOpicking.star contains particle coordinates picked by CRYOLO (X and Y in 1st and 2nd columns; remainder of .star file is output of RELION particle extraction job, extracted particles not deposited here)","image_width":"3838","image_height":"3710"},{"segmentations":[],"name":"Dataset 5 of human pre-B spliceosome; motion-corrected micrographs","directory":"data/MotionCorr/job1163/Movies_9Feb","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":3234,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.022,"pixel_height":1.022,"micrographs_file_pattern":"data/MotionCorr/job1163/Movies_9Feb/FoilHole_*_Data_*_*_201902*_*-*.mrc","picked_particles_file_pattern":"data/dataset5_gautomatchpicking.star","picked_particles_directory":"data","details":"Micrographs were averaged using RELION 3.0 implementation of MotionCor2 with 5x5 patches and dose-weighting. Original movies were 40 frames with a total dose of 44 electrons per squared Angstrom over 6 seconds.\nData collected on Titan Krios 3 at the MRC Laboratory of Molecular Biology on a K2 detector operated in counting mode.\ndataset5_gautomatchpicking.star contains particle coordinates picked by Gautomatch using templates from pre-B complex 2D averages from the other 4 datasets (X and Y in 1st and 2nd columns; remainder of .star file is output of RELION particle extraction job, extracted particles not deposited here)","image_width":"3838","image_height":"3710"},{"segmentations":[],"name":"Selected U4/U6.U5 tri-snRNP particles after Bayesian polishing","directory":"data/Polish","category":"picked particles - single frame - processed","header_format":"MRCS","data_format":"MRCS","num_images_or_tilt_series":20537,"frames_per_image":585488,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.022,"pixel_height":1.022,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Particles from datasets 2, 3, and 4 were picked with CRYOLO (see dataset*_CRYOLOpicking.star) and 3D classified. Tri-snRNP and pre-B particles were selected, CTF-refined and subjected to Bayesian polishing in RELION 3.0, giving the particle stacks in Polish/\nA further round of CTF refinement produced the reconstruction deposited in the EMDB as EMD-4658, with the resultant run_data.star file deposited here as \"trisnRNP_EMD4658_refine_data.star\"\n\nFurther classification of these particles yielded various other deposited maps, metadata for which are deposited here. In summary:\n\n\"preB_unshiftedbox_EMD4665_refine_data.star\"\nThe subset of these polished tri-snRNP particles that correspond to pre-B complex, corresponds to EMD-4665\n\n\"trisnRNP_prp28class_EMD4686_refine_data.star\"\nSubset of tri-snRNP with strong Prp28, corresponds to EMD-4686\n\n\"trisnRNP_U540Kclass_refine_data.star\"\nSubset of tri-snRNP with strong U5-40K\n\nFor full details see Charenton et al Science 2019.","image_width":"420","image_height":"420"},{"segmentations":[],"name":"Crude shifted preB particles","directory":"data/Extract","category":"picked particles - single frame - unprocessed","header_format":"MRCS","data_format":"MRCS","num_images_or_tilt_series":873597,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.7033,"pixel_height":1.7033,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Particles from all datasets were picked (see dataset*_*picking.star) and 3D classified using a tri-snRNP reference. Tri-snRNP and pre-B particles were selected and re-extracted with a \"shifted box\" such that the box would encompass the full pre-B complex. Particles were also scaled down to 1.7033 Ångstrom per pixel.\nFurther rounds of 3D classification produced a crude set of 117,284 pre-B particles, metadata in the deposited preB_allparticles_shiftedbox_refine_data.star\nFurther classification of these particles yielded various deposited maps, metadata for which are deposited here. In summary:\n\n\"preB_prp4kclass_EMD4688_refine_data.star\"\nThe subset of pre-B particles with strong density for Prp4 kinase, corresponds to EMD-4688\n\n\"preB_U1class_EMD4687_refine_data.star\"\nThe subset of pre-B particles with strong density for U1 snRNP, corresponds to EMD-4687\n\n\"preB_U2class_EMD4690_refine_data.star\"\nThe subset of pre-B particles with strong density for U2 snRNP, corresponds to EMD4690","image_width":"360","image_height":"360"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Human pre-B spliceosome and U4/U6.U5 tri-snRNP","principal_investigator":[{"author_orcid":"0000-0003-1785-6510","middle_name":null,"organization":"MRC Laboratory of Molecular Biology","street":"Francis Crick Avenue","town_or_city":"Cambridge","state_or_province":"Cambridgeshire","post_or_zip":"CB2 0QH","telephone":null,"fax":null,"first_name":"Kiyoshi","last_name":"Nagai","email":"kn [at] mrc-lmb.cam.ac.uk","country":"United Kingdom","entry":"EMPIAR-10307"}],"status":"REL","deposition_date":"2019-04-12","release_date":"2019-09-30","obsolete_date":null,"update_date":"2019-09-30","corresponding_author":{"author":{"author_orcid":"0000-0003-4738-9503","middle_name":null,"organization":"MRC Laboratory of Molecular Biology; University of Cambridge","street":"Francis Crick Avenue","town_or_city":"Cambridge","state_or_province":"Cambridgeshire","post_or_zip":"CB2 0QH","first_name":"Max","last_name":"Wilkinson","country":"United Kingdom"}},"authors":[{"author":{"name":"Charenton C","author_orcid":"0000-0002-8959-7012"}},{"author":{"name":"Wilkinson ME","author_orcid":"0000-0003-4738-9503"}},{"author":{"name":"Nagai K","author_orcid":"0000-0003-1785-6510"}}],"cross_references":["EMD-4689","EMD-4687","EMD-4676","EMD-4686","EMD-4673","EMD-4672","EMD-4675","EMD-4688","EMD-4690","EMD-4674"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Charenton C","author_orcid":"0000-0002-8959-7012"},{"name":"Wilkinson ME","author_orcid":"0000-0003-4738-9503"},{"name":"Nagai K","author_orcid":"0000-0003-1785-6510"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Mechanism of 5' splice site transfer for human spliceosome activation","volume":"364","country":"","first_page":"362","last_page":"367","year":"2019","language":"English","doi":"10.1126/science.aax3289","pubmedid":"30975767","details":"5 datasets containing collectively 28,705 multi-frame micrographs after motion correction and dose-weighting.\nAlso contains particle coordinates, polished particles for the human tri-snRNP, unpolished particles for pre-B complex, and metadata star files from various refinements in Relion.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Science (New York, N.Y.)","journal_abbreviation":"Science","issue":"6438","preprint":false}],"dataset_size":"2.3 TB","experiment_type":"EMDB","scale":null,"entry_doi":"10.6019/EMPIAR-10307"}}