{ "code": "SASDB88", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.", "publication": { "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.", "author_list": "Shah N, Beckham SA, Wilce JA, Wilce MCJ", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkx1307", "pmid": "29346611", "published_date": "2018 Apr 6" }, "status": "released", "submitted_date": "2016-12-11", "released_date": "2018-01-22" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB88.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB88.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB88_dat_img.png", "intensities_kratky_plot": 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"O95786", "uniprot_range_first": 1, "uniprot_range_last": 925, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": 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"number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Melbourne, Australia", "full_name": "Monash University", "webpage": "http://www.monash.edu/" } ], "contributor_name": "Neelam", "contributor_surname": "Shah", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-11-20", "storage_temperature": 4.0, "cell_temperature": 15.0, "exposure_time": 2.0, "number_of_frames": 13, "wavelength": 0.10332, "sample_detector_distance": 1.6, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.076, "s_max": 2.506, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB88_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "v2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB88_fit1_model1.pdb", "model_mw": 99.03, "bead_radius": null, "log": null, "symmetry": "p1", "comment": "", "user": 168 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB88_fit1_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "v2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB88_fit1_model2.pdb", "model_mw": 99.03, "bead_radius": null, "log": null, "symmetry": "p1", "comment": "", "user": 168 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB88_fit1_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "v2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB88_fit1_model3.pdb", "model_mw": 99.03, "bead_radius": null, "log": null, "symmetry": "p1", "comment": "", "user": 168 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB88_fit1_fit_img.png", "software": null, "chi_square_value": 0.32, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB88_fit1.fit", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB88_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "v1.1.2", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB88_fit2_model1.pdb", "model_mw": 136.864, "bead_radius": 3.75, "log": null, "symmetry": "p1", "comment": "", "user": 168 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB88_fit2_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.289, "p_value": 0.010145, "fit_residual_plot": "SASDB88_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB88_fit2.fir", "fit_log": null, "software_version": "v1.1.2", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM v4.5", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx in 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH 7.4 were collected using size exclusion chromatography (SEC-SAXS) on the SAXS/WAXS camera on the storage ring Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Data frames (13 x 2 s exposures) were collected through the SEC elution peak at 33.2 min (GE Healthcare Life Sciences Superdex 200 10/300; 0.4 ml/min; 100 μl injection at 8 mg/ml). The data were normalized to the intensity of the transmitted beam and radially averaged; the radially averaged scattering of the solvent-blank was subtracted and the different curves were scaled to yield the final composite scattering curve. The SAXS data were collected at 15 °C.", "tags": [], "intensity_unit": null, "experimental_mw": 108.1, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 112.0, "porod_mw_error": null, "pddf_i0": 0.0516, "pddf_i0_error": null, "guinier_i0": 0.051, "guinier_i0_error": null, "pddf_rg": 4.34, "pddf_rg_error": null, "guinier_rg": 4.19, "guinier_rg_error": null, "pddf_dmax": 15.6, "pddf_dmax_error": null, "porod_volume": 189.99, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 58, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDB88_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }