The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDC67",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Structural model of human dUTPase in complex with a novel proteinaceous inhibitor.",
"publication": {
"title": "Structural model of human dUTPase in complex with a novel proteinaceous inhibitor.",
"author_list": "Nyíri K, Mertens HDT, Tihanyi B, Nagy GN, Kőhegyi B, Matejka J, Harris MJ, Szabó JE, Papp-Kádár V, Németh-Pongrácz V, Ozohanics O, Vékey K, Svergun DI, Borysik AJ, Vértessy BG",
"journal": "Sci Rep",
"doi": "10.1038/s41598-018-22145-8",
"pmid": "29531348",
"published_date": "2018 Mar 12"
},
"status": "released",
"submitted_date": "2017-08-10",
"released_date": "2018-02-27"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC67.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC67.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC67_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC67_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC67_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC67_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC67.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "SaPIbov1 pathogenicity island repressor",
"short_name": "Stl",
"sequence": "GSPEFSM\r\nEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLYDETIKLLELLKESKINVNDIDYDYVLKLYKQILSTDTEKSIINYETLANTRKSSDKKREVTIEEIGEFHEKYLKLLFTNLETHNDRKKALAEIEKLKEESIYLGEKLRLVPNHHYDAIKGKPMYKLYLYEYPDRLEHQKKIILEKDTN",
"organism": "Staphylococcus aureus",
"uniprot_code": "E2FZP6",
"uniprot_range_first": 13,
"uniprot_range_last": 278,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MRYFFRYDIIWIEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENG\nNRNIGVNEIEIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFAKFDKMYSYVNKAYYNDG\nDIYYSSYDLYDETIKLLELLKESKINVNDIDYDYVLKLYKQILSTDTEKSIINYETLANT\nRKSSDKKREVTIEEIGEFHEKYLKLLFTNLETHNDRKKALAEIEKLKEESIYLGEKLRLV\nPNHHYDAIKGKPMYKLYLYEYPDRLEHQKKIILEKDTN",
"mw": 32.016,
"total_mw": 64.032,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES 300 mM NaCl 5 mM MgCl2",
"concentration_unit": null,
"comment": "Buffer B",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "SaPIbov1 pathogenicity island repressor",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": 38738,
"absorbption": null,
"deuteration": null,
"mixture": false
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Haydyn",
"contributor_surname": "Mertens",
"orcid": null
}
],
"concentration_method": "A280",
"concentration_unit": null,
"date": "2016-07-09",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
"concentration_min": 0.2,
"concentration_max": 0.9,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.118,
"s_max": 5.031,
"total_exposure_time": 1.0,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC67_fit1_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC67_fit1_model1.pdb",
"model_mw": 62.82,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": "server address: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index",
"user": 12
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC67_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.756,
"p_value": 0.01337,
"fit_residual_plot": "SASDC67_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC67_fit1.fit",
"fit_log": null,
"software_version": "2.9.0",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC67_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.9.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC67_fit2_model1.pdb",
"model_mw": 30.7,
"bead_radius": 2.2,
"log": null,
"symmetry": "P2",
"comment": "",
"user": 12
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC67_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.605,
"p_value": 0.440167,
"fit_residual_plot": "SASDC67_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC67_fit2.fir",
"fit_log": null,
"software_version": "2.9.0",
"description": null
}
],
"estimated_volume_method": "DAM volume",
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "2.9.0",
"i0_calibration_standard": "BSA",
"description": null,
"experiment_description": null,
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 45.0,
"experimental_mw_error": 5.0,
"guinier_i0_mw": 45.0,
"guinier_i0_mw_error": 5.0,
"porod_mw": 59.0,
"porod_mw_error": 6.0,
"pddf_i0": 0.032,
"pddf_i0_error": 0.001,
"guinier_i0": 0.031,
"guinier_i0_error": 0.001,
"pddf_rg": 3.2,
"pddf_rg_error": 0.1,
"guinier_rg": 3.3,
"guinier_rg_error": 0.1,
"pddf_dmax": 10.5,
"pddf_dmax_error": 0.5,
"porod_volume": 100.0,
"porod_volume_error": 20.0,
"estimated_volume": 90.0,
"estimated_volume_error": 20.0,
"guinier_point_first": 1,
"guinier_point_last": 93,
"pddf_point_first": 10,
"pddf_point_last": 1200,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDC67_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
