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{
"code": "SASDF65",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.",
"publication": {
"title": "Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.",
"author_list": "Srivastava D, Gakhar L, Artemyev NO",
"journal": "Nat Commun",
"doi": "10.1038/s41467-019-11088-x",
"pmid": "31300652",
"published_date": "2019 Jul 12"
},
"status": "released",
"submitted_date": "2019-03-27",
"released_date": "2019-06-17"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF65.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF65.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF65_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF65.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
}
],
"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) amino acids 1-492",
"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": 25.0,
"exposure_time": 0.5,
"number_of_frames": null,
"wavelength": 0.1033,
"sample_detector_distance": 3.5,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.054,
"s_max": 3.813,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit1_model1_img.png",
"software": "BILBOMD",
"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/SASDF65_fit1_model1.pdb",
"model_mw": 55.35,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "One state model",
"user": 431
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF65_single_state_model_corrected_fitfoxs_img.png",
"software": "FoXS",
"chi_square_value": 1.507476,
"p_value": 0.000294,
"fit_residual_plot": "SASDF65_single_state_model_corrected_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF65_fit1.dat",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model1_img.png",
"software": "BILBOMD",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model1.pdb",
"model_mw": 137.9,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Fractional contribution in X-ray scattering: 59%",
"user": 431
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model2_img.png",
"software": "BILBOMD",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model2.pdb",
"model_mw": 137.9,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Fractional contribution in X-ray scattering: 29%",
"user": 431
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model3_img.png",
"software": "BILBOMD",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model3.pdb",
"model_mw": 137.9,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Fractional contribution in X-ray scattering: 12%",
"user": 431
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF65_multi_state_model_corrected_fitfoxs_img.png",
"software": "MES-FoXS",
"chi_square_value": 1.198522,
"p_value": 0.004708,
"fit_residual_plot": "SASDF65_multi_state_model_corrected_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF65_fit2.dat",
"fit_log": null,
"software_version": null,
"description": "Three state model, the fractional contributions in X-ray scattering from the first, second and third states are 0.59, 0.29 and 0.12 respectively."
}
],
"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 Ric8a 1-492 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 (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 25°C. 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": 64.6,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 55.0,
"porod_mw_error": null,
"pddf_i0": 0.002138,
"pddf_i0_error": null,
"guinier_i0": 0.00212099,
"guinier_i0_error": 2e-06,
"pddf_rg": 3.5,
"pddf_rg_error": null,
"guinier_rg": 3.37,
"guinier_rg_error": 0.1,
"pddf_dmax": 12.7,
"pddf_dmax_error": null,
"porod_volume": 88.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 25,
"guinier_point_last": 111,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF65_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
