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": "SASDGB6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A.",
"publication": {
"title": "Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A.",
"author_list": "Srivastava D, Artemyev NO",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.AC119.011135",
"pmid": "31624147",
"published_date": "2019 Oct 17"
},
"status": "released",
"submitted_date": "2019-09-26",
"released_date": "2019-11-04"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGB6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGB6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGB6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGB6.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": "Resistance to inhibitors of cholinesterase 8 homolog A",
"short_name": "Ric8a",
"sequence": "GHMADPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\r\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\r\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\r\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\r\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\r\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\r\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\r\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\r\nKLVNMFDKLSRH",
"organism": "Bos taurus",
"uniprot_code": "Q5E9J8",
"uniprot_range_first": 1,
"uniprot_range_last": 492,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MEPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\nKLVNMFDKLSRHRVIQPMGMSPRGQLTSLQDAMCETMEGQLSSDPDSDPD",
"mw": 55.643,
"total_mw": 55.643,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "miniGi",
"short_name": null,
"sequence": "AMEKAAREVKLLLLGADNSGKSTIVKQMKIIHEAGEYMPMERVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEDVAAIIFCVDLSDYEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 24.54,
"total_mw": 24.54,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Resistance to inhibitors of cholinesterase 8 homolog A (Ric8A) miniGi complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Iowa, USA",
"full_name": "University of Iowa",
"webpage": "https://uiowa.edu/"
}
],
"contributor_name": "Dhiraj",
"contributor_surname": "Srivastava",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-10-27",
"storage_temperature": 4.0,
"cell_temperature": null,
"exposure_time": 0.5,
"number_of_frames": null,
"wavelength": null,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 250.0,
"flow_rate": 0.9,
"s_min": 0.039,
"s_max": 3.813,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGB6_fit1_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6n85",
"ext_code": "6N85",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGB6_fit1_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 431
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/86900_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.637,
"p_value": 0.0,
"fit_residual_plot": "86900_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGB6_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/86900.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGB6_fit2_model1_img.png",
"software": "Rosetta",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "Rosetta",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGB6_fit2_model1.pdb",
"model_mw": 79.71,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 431
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/73700_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.882,
"p_value": 0.0,
"fit_residual_plot": "73700_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGB6_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/73700.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": "Purified Ric8a1-492 was mixed with excess of purified miniGi and the complex was purified by size-exclusion chromatography (SEC). The complex fractions were pooled together, concentrated and additional SEC-SAXS data was collected as described above. X-ray wavelength = UNKNOWN.",
"experiment_description": "Synchrotron SAXS data from solutions of the Ric8A-miniGi complex in 20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory storage ring (Lemont, IL, USA) using a Pilatus3 X 1M detector (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 250.00 μl sample at 10 mg/ml was injected at a 0.90 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column . The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 83.6,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.00261,
"pddf_i0_error": 1.93e-06,
"guinier_i0": 0.0026,
"guinier_i0_error": 2.65e-06,
"pddf_rg": 3.28,
"pddf_rg_error": 0.003,
"guinier_rg": 3.24,
"guinier_rg_error": 0.006,
"pddf_dmax": 10.7,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 13,
"guinier_point_last": 118,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDGB6_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-01-04T14:24:46.462986+01:00",
"bragg_peak": []
}
