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{
"code": "SASDXT3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural Dynamics of Dengue Virus UTRs and Their Cyclization.",
"publication": {
"title": "Structural Dynamics of Dengue Virus UTRs and Their Cyclization.",
"author_list": "Robinson ZE, Pereira HS, D'Souza MH, Patel TR",
"journal": "Biophys J",
"doi": "10.1016/j.bpj.2025.09.004",
"pmid": "40914810",
"published_date": "2025 Sep 5"
},
"status": "released",
"submitted_date": "2025-04-10",
"released_date": "2025-09-09"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXT3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXT3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXT3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXT3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXT3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXT3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXT3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"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": "DENV2 RNA, 5' Untranslated region",
"short_name": "DENV2 5' UTR",
"sequence": "GGAGUUGUUAGUCUACGUGGACCGACAAAGACAGAUUCUUUGAGGGAGCUAAGCUCAACGUAGUUCUAACAGUUUUUUAAUUAGAGAGCAGAUCUCUGAUGAAUAACCAACGGAAAAAGGCGAAAAACACGCCUUUCAAUAUGCUGAAACGCGAGAGAAACCAUCUGUUCCAUCUGUU",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": "",
"mw": 57.403,
"total_mw": 57.403,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.0,
"deuteration": null
},
"purity_method": null,
"name": "Dengue Virus 2 (DENV2) RNA, 5' Untranslated region",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Lethbridge, AB, Canada",
"full_name": "University of Lethbridge",
"webpage": "http://www.uleth.ca/"
}
],
"contributor_name": "Trushar",
"contributor_surname": "Patel",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2023-09-08",
"storage_temperature": -80.0,
"cell_temperature": 25.0,
"exposure_time": 3.0,
"number_of_frames": 600,
"wavelength": 0.094,
"sample_detector_distance": 3.7,
"concentration_min": null,
"concentration_max": 0.7,
"sample_volume": 60.0,
"flow_rate": 0.16,
"s_min": 0.045,
"s_max": 3.4,
"total_exposure_time": null,
"seccolumn": 19
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXT3_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXT3_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 2.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 239
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXT3_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.125,
"p_value": 0.0569,
"fit_residual_plot": "SASDXT3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXT3_fit1.fir",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXT3_fit2_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXT3_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 2.9,
"log": null,
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"comment": null,
"user": 239
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXT3_fit2_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.125,
"p_value": 0.0569,
"fit_residual_plot": "SASDXT3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXT3_fit2.fir",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXT3_fit3_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXT3_fit3_model1.pdb",
"model_mw": null,
"bead_radius": 2.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 239
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXT3_fit3_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.125,
"p_value": 0.0569,
"fit_residual_plot": "SASDXT3_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXT3_fit3.fir",
"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": null,
"experiment_description": "Synchrotron SAXS data from solutions of the 5' Untranslated region of DENV2 RNA in 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH 6 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 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 60.00 μl sample at 0.7 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 25°C. 600 successive 3 second frames were collected. 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": "1/cm",
"experimental_mw": 44.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.007147,
"pddf_i0_error": null,
"guinier_i0": 0.00717869,
"guinier_i0_error": null,
"pddf_rg": 3.77,
"pddf_rg_error": null,
"guinier_rg": 3.681,
"guinier_rg_error": 0.256,
"pddf_dmax": 11.5,
"pddf_dmax_error": null,
"porod_volume": 66.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 34,
"guinier_point_last": 278,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDXT3_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-09-09T12:07:09.896001+02:00",
"bragg_peak": []
}
