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": "SASDGA5",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural basis of cell surface signaling by a conserved sigma regulator in Gram-negative bacteria.",
"publication": {
"title": "Structural basis of cell surface signaling by a conserved sigma regulator in Gram-negative bacteria.",
"author_list": "Jensen JL, Jernberg BD, Sinha S, Colbert CL",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.RA119.010697",
"pmid": "32107313",
"published_date": "2020 Feb 26"
},
"status": "released",
"submitted_date": "2019-09-16",
"released_date": "2020-03-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGA5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGA5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGA5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGA5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 1M",
"resolution": 0.172
},
"name": "Advanced Photon Source (APS), Argonne National Laboratory",
"city": "Lemont, IL",
"country": "USA",
"beamline_name": "BioCAT 18ID",
"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": "PupR protein",
"short_name": "PupR",
"sequence": "GAMGQDWRADYHSRIGEQRRLTLADGTQVQLNTDSALNVA\r\nFDQQARRLRLVRGEMLITRPALADSRPLWVDTEHGRLESTL\r\nAQFNVRLHGQHTQATVYQGSVALQPALHAYPPILLGAGEQA\r\nSFNQQGLLARQAVAAVAPAWSQGMLVAQGQPLAAFIEDLAR\r\nYRRGHLACDPALAGLRVSGTFPLENTDKIIAAVAETLQLEVQ\r\nHFTRYWVTLKPRMA",
"organism": "Pseudomonas putida",
"uniprot_code": "Q52209",
"uniprot_range_first": 110,
"uniprot_range_last": 324,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MNGQGATSIPGEVAEQAMHWHLELQEPAVSAATLAACMSWRQAHPLHEHAWQRTQVFAQR\nLREMRSPGQRPLAHAALRPQQSRRTALKQLSLLMAAGAGAWYLKDAALVQDWRADYHSRI\nGEQRRLTLADGTQVQLNTDSALNVAFDQQARRLRLVRGEMLITRPALADSRPLWVDTEHG\nRLESTLAQFNVRLHGQHTQATVYQGSVALQPALHAYPPILLGAGEQASFNQQGLLARQAV\nAAVAPAWSQGMLVAQGQPLAAFIEDLARYRRGHLACDPALAGLRVSGTFPLENTDKIIAA\nVAETLQLEVQHFTRYWVTLKPRMA",
"mw": 24.124,
"total_mw": 24.124,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM HEPES 400 mM LiCl 10% v/v glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "The C-terminal cell-surface signaling domain of the Pseudomonas capeferrum anti-sigma regulator PupR",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Vanderbilt University",
"webpage": null
}
],
"contributor_name": "Jaime",
"contributor_surname": "Jensen",
"orcid": "https://orcid.org/0000-0002-8818-7513"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-03-16",
"storage_temperature": null,
"cell_temperature": 25.0,
"exposure_time": null,
"number_of_frames": null,
"wavelength": 0.103,
"sample_detector_distance": 3.5,
"concentration_min": null,
"concentration_max": 9.6,
"sample_volume": 500.0,
"flow_rate": 0.6,
"s_min": 0.262,
"s_max": 3.665,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGA5_fit1_model1_img.png",
"software": "MultiFoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGA5_fit1_model1.pdb",
"model_mw": 23.59,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 490
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGA5_fit1_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 1.5473,
"p_value": 0.000262,
"fit_residual_plot": "SASDGA5_fit1_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGA5_fit1.dat",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGA5_fit2_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGA5_fit2_model1.pdb",
"model_mw": 23.74,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 490
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGA5_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 4.862,
"p_value": 0.0,
"fit_residual_plot": "SASDGA5_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGA5_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGA5_fit3_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "DAMFILT 5.0 (r4547)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGA5_fit3_model1.pdb",
"model_mw": 26.604,
"bead_radius": 2.0,
"log": null,
"symmetry": null,
"comment": null,
"user": 490
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGA5_fit3_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.456,
"p_value": 0.998201,
"fit_residual_plot": "SASDGA5_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGA5_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 the C-terminal cell-surface signaling domain of PupR in 25 mM HEPES 400 mM LiCl 10% v/v glycerol, pH 7.5 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.103 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 500.00 μl sample at 9.6 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 25°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of an appropriate solvent-blank was subtracted from the SEC elution peak of the sample.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 26.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 29.0,
"porod_mw_error": null,
"pddf_i0": 17.45,
"pddf_i0_error": null,
"guinier_i0": 17.6,
"guinier_i0_error": 0.05,
"pddf_rg": 2.23,
"pddf_rg_error": null,
"guinier_rg": 2.23,
"guinier_rg_error": 0.1,
"pddf_dmax": 7.5,
"pddf_dmax_error": null,
"porod_volume": 48.6,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 106,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDGA5_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-03-03T14:59:07.808703+01:00",
"bragg_peak": []
}
