{ "code": "SASDF85", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Structural Insights Into the Transcriptional Regulation of HigBA Toxin–Antitoxin System by Antitoxin HigA in Pseudomonas aeruginosa", "publication": { "title": "Structural Insights Into the Transcriptional Regulation of HigBA Toxin–Antitoxin System by Antitoxin HigA in Pseudomonas aeruginosa", "author_list": "Liu Y, Gao Z, Liu G, Geng Z, Dong Y, Zhang H", "journal": "Frontiers in Microbiology", "doi": "10.3389/fmicb.2019.03158", "pmid": null, "published_date": "2020 Jan 22" }, "status": "released", "submitted_date": "2019-04-04", "released_date": "2020-01-24" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF85.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF85.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF85_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF85_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF85_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF85_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF85.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Shanghai Synchrotron Radiation Facility (SSRF)", "city": "Shanghai", "country": "China", "beamline_name": "BL19U2", "beam_geometry": "", "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": "Uncharacterized protein", "short_name": null, "sequence": "MATNGMRPIHPGEILRDEFLMEFDISPAALARALKVSAPTVNDIVREQRGISADMAIRLG\r\nRYFDTSAQFWMNLQSEYSLATAYAANGKQIEHEIEPLLAHG", "organism": "Pseudomonas aeruginosa", "uniprot_code": "Q9HVC1", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MATNGMRPIHPGEILRDEFLMEFDISPAALARALKVSAPTVNDIVREQRGISADMAIRLG\nRYFDTSAQFWMNLQSEYSLATAYAANGKQIEHEIEPLLAHG", "mw": 11.248, "total_mw": 22.496, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 300 mM NaCl, 5% (v/v) glycerol, and 1 mM PMSF", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Pseudomonas aeruginosa antitoxin HigA: apo PaHigA", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Shanghai, China", "full_name": "National Center for Protein Science Shanghai", "webpage": "http://www.sibcb-ncpss.org" } ], "contributor_name": "Guangfeng", "contributor_surname": "Liu", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-12-21", "storage_temperature": 10.0, "cell_temperature": 23.0, "exposure_time": 1.0, "number_of_frames": 20, "wavelength": 0.103, "sample_detector_distance": 2.7, "concentration_min": 1.0, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.118, "s_max": 3.399, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF85_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF85_fit1_model1.pdb", "model_mw": 14.759, "bead_radius": 1.75, "log": "https://www.sasbdb.org/media/log_files/merge_001.log", "symmetry": "p1", "comment": null, "user": 434 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF85_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.064, "p_value": 0.797881, "fit_residual_plot": "SASDF85_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF85_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/merge_001.log", "software_version": "2.8.4", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF85_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "6jpi", "ext_code": "6JPI", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF85_fit2_model1.pdb", "model_mw": 20.8, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 434 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF85_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 2.034, "p_value": 0.0, "fit_residual_plot": "SASDF85_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF85_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dimer.log", "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 apo PaHigA in 20 mM Tris, 300 mM NaCl, 5% (v/v) glycerol, 1 mM PMSF, pH 8 were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 23°C. 20 successive 1 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 22.1, "experimental_mw_error": null, "guinier_i0_mw": 22.1, "guinier_i0_mw_error": 2.0, "porod_mw": 18.4, "porod_mw_error": null, "pddf_i0": 18.9, "pddf_i0_error": null, "guinier_i0": 18.77, "guinier_i0_error": 0.04, "pddf_rg": 2.02, "pddf_rg_error": null, "guinier_rg": 1.967, "guinier_rg_error": 0.007, "pddf_dmax": 6.6, "pddf_dmax_error": null, "porod_volume": 23.2, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 26, "guinier_point_last": 139, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF85_datloglog_img.png", "symmetry": null, "last_modified": "2020-01-24T10:36:55.405527+01:00", "bragg_peak": [] }