{ "code": "SASDWR3", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Alu RNA pseudoknot alterations influence SRP9/SRP14 association.", "publication": { "title": "Alu RNA pseudoknot alterations influence SRP9/SRP14 association.", "author_list": "Gussakovsky D, Brown MJF, Pereira HS, Meier M, Padilla-Meier GP, Black NA, Booy EP, Stetefeld J, Patel TR, McKenna SA", "journal": "RNA", "doi": "10.1261/rna.080359.124", "pmid": "40345827", "published_date": "2025 May 9" }, "status": "released", "submitted_date": "2024-05-24", "released_date": "2025-05-31" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWR3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWR3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWR3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWR3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWR3.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": "BC120 G25C RNA", "short_name": null, "sequence": "GGCCGGGCGCGGUGGCUCACGCCUCUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUUU", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": "", "mw": 38.855, "total_mw": 38.855, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "phosphate buffered saline", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "BC120 G25C RNA", "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": "2023-09-22", "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": 3.0, "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/SASDWR3_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/SASDWR3_fit1_model1.pdb", "model_mw": null, "bead_radius": 3.5, "log": null, "symmetry": null, "comment": null, "user": 239 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR3_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.126, "p_value": 0.0302, "fit_residual_plot": "SASDWR3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR3_fit1.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWR3_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/SASDWR3_fit2_model1.pdb", "model_mw": null, "bead_radius": 3.5, "log": null, "symmetry": null, "comment": null, "user": 239 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR3_fit2_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.124, "p_value": 0.0302, "fit_residual_plot": "SASDWR3_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR3_fit2.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWR3_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/SASDWR3_fit3_model1.pdb", "model_mw": null, "bead_radius": 3.5, "log": null, "symmetry": null, "comment": null, "user": 239 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWR3_fit3_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.121, "p_value": 0.0302, "fit_residual_plot": "SASDWR3_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWR3_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 BC120 G25C RNA in phosphate buffered saline, pH 7.4 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 3 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": 45.43, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 31.5, "porod_mw_error": null, "pddf_i0": 0.05822, "pddf_i0_error": null, "guinier_i0": 0.0575753, "guinier_i0_error": null, "pddf_rg": 4.3, "pddf_rg_error": null, "guinier_rg": 4.086, "guinier_rg_error": 0.11, "pddf_dmax": 13.83, "pddf_dmax_error": null, "porod_volume": 63.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 40, "guinier_point_last": 198, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDWR3_datloglog_img.png", "symmetry": null, "last_modified": "2025-05-31T21:41:25.054885+02:00", "bragg_peak": [] }