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{
"code": "SASDF95",
"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/SASDF95.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF95.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF95_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF95_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF95_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF95_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF95.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
},
{
"long_name": "DNA Duplex",
"short_name": null,
"sequence": "TGAAGTTAACGCTTAACGTTAAGGGTTAATGA",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 10.006,
"total_mw": 20.012,
"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 bound to duplex DNA: PaHigA-DNA complex",
"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": "2018-09-19",
"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": 0.07,
"s_max": 3.348,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF95_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/SASDF95_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 3.0,
"log": "https://www.sasbdb.org/media/log_files/AO28.log",
"symmetry": "p1",
"comment": null,
"user": 434
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF95_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.053,
"p_value": 0.01926,
"fit_residual_plot": "SASDF95_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF95_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/AO28.log",
"software_version": "2.8.4",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF95_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/SASDF95_fit2_model1.pdb",
"model_mw": 58.78,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/4D.log",
"symmetry": null,
"comment": null,
"user": 434
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF95_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 6.229,
"p_value": 0.0,
"fit_residual_plot": "SASDF95_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF95_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4D.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 the PaHigA-DNA complex 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": 73.8,
"experimental_mw_error": null,
"guinier_i0_mw": 73.8,
"guinier_i0_mw_error": 1.2,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 80.36,
"pddf_i0_error": null,
"guinier_i0": 80.36,
"guinier_i0_error": 0.17,
"pddf_rg": 2.98,
"pddf_rg_error": null,
"guinier_rg": 2.935,
"guinier_rg_error": 0.008,
"pddf_dmax": 9.83,
"pddf_dmax_error": null,
"porod_volume": 81.1,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 34,
"guinier_point_last": 95,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF95_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-01-24T10:37:27.754832+01:00",
"bragg_peak": []
}
