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{
"code": "SASDWR5",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "A new protein-dependent riboswitch activates ribosomal frameshifting",
"publication": {
"title": "A new protein-dependent riboswitch activates ribosomal frameshifting",
"author_list": "Betts J, Jeffries C, Passchier T, Kung H, Graham S, Abdelhamid M, Howard J, Craggs T, Graham S, Brierley I, Leake M, Quinn S, Hill C",
"journal": null,
"doi": "10.1101/2025.07.17.665365",
"pmid": null,
"published_date": "2025 Jul 18"
},
"status": "released",
"submitted_date": "2025-04-01",
"released_date": "2025-07-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWR5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWR5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWR5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWR5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Stimulatory element RNA",
"short_name": null,
"sequence": "CCACAAGGUGCGGUGCUAACUAAAUCCCUAGCACCCC",
"organism": "synthetic RNA",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": "",
"mw": 11.836,
"total_mw": 11.836,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Single-stranded RNA"
}
],
"buffer": {
"name": "20 mM HEPES pH 7.4, 400 mM KCl 2% v/v glycerol, 1 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": null,
"deuteration": null
},
"purity_method": null,
"name": "Stimulatory element RNA",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2021-04-26",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 0.25,
"number_of_frames": 57,
"wavelength": 0.123983,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 7.08,
"sample_volume": 50.0,
"flow_rate": 0.35,
"s_min": 0.026,
"s_max": 7.413,
"total_exposure_time": null,
"seccolumn": 4
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWR5_fit1_model1_img.png",
"software": "SREFLEX",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWR5_fit1_model1.pdb",
"model_mw": 11.39,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/rc01-6b_m4a00.log",
"symmetry": null,
"comment": "AlphaFold model with SREFLEX refinement",
"user": 9
},
{
"model_plot": null,
"software": "Other [static image]",
"pdb_link": [],
"model_title": null,
"type_of_model": "other",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWR5_fit1_model2.png",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR5_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.11,
"p_value": 0.1916,
"fit_residual_plot": "SASDWR5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR5_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWR5_fit2_model1_img.png",
"software": "MONSA",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWR5_fit2_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/RNASL4.log",
"symmetry": null,
"comment": "Single MONSA reconstruction",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR5_fit2_fixed_fit_img.png",
"software": "MONSA",
"chi_square_value": 1.101,
"p_value": 0.0808,
"fit_residual_plot": "SASDWR5_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR5_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWR5_fit3_model1_img.png",
"software": "Coot",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWR5_fit3_model1.pdb",
"model_mw": 11.38,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/RNA200.log",
"symmetry": null,
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR5_fit3_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 13.95,
"p_value": 0.0,
"fit_residual_plot": "SASDWR5_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR5_fit3.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The models displayed in this entry show: Top: A post normal-mode SREFLEX model obtained using an AlphaFold-predicted structure of the RNA as an initial template, and an alignment of several different SREFLEX outputs. Middle: a MONSA ab initio dummy-atom model reconstruction of the RNA particle. Bottom: A pseudoknot conformation based on the X-ray crystal structure of the RNA in complex with Protein 2A (refer to SASBDB entry SASDWS5; https://www.sasbdb.org/data/SASDWS5). The full entry archive contains the unsubtracted SEC-SAXS 1D-data frames in addition to DAMMIN, MONSA and SREFLEX modelling routines.",
"experiment_description": "Synchrotron SAXS data from solutions of stimulatory element RNA in 20 mM HEPES pH 7.4, 400 mM KCl 2% v/v glycerol, 1 mM DTT were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123983 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 7.1 mg/ml was injected at a 0.35 ml/min flow rate onto a GE Superdex 75 Increase 5/150 column at 20°C. 57 successive 0.250 second frames were collected through the SEC-elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 13.5,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 10.0,
"porod_mw_error": null,
"pddf_i0": 7577.0,
"pddf_i0_error": null,
"guinier_i0": 7530.62,
"guinier_i0_error": null,
"pddf_rg": 1.989,
"pddf_rg_error": null,
"guinier_rg": 1.922,
"guinier_rg_error": 0.003,
"pddf_dmax": 8.0,
"pddf_dmax_error": null,
"porod_volume": 18.9,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 49,
"guinier_point_last": 221,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDWR5_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-07-20T11:29:02.233366+02:00",
"bragg_peak": []
}
