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": "SASDCS6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology.",
"publication": {
"title": "Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology.",
"author_list": "White MA, Tsalkova T, Mei FC, Cheng X",
"journal": "Cells",
"doi": "10.3390/cells9010035",
"pmid": "31877746",
"published_date": "2019 Dec 21"
},
"status": "released",
"submitted_date": "2017-07-27",
"released_date": "2019-12-02"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCS6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCS6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCS6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCS6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 100K",
"resolution": 172.0
},
"name": "Sealy Center For Structural Biology, UTMB-G",
"city": "Galveston, TX",
"country": "USA",
"beamline_name": "Rigaku BioSAXS-1000",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Rap guanine nucleotide exchange factor 3",
"short_name": "EPAC1B",
"sequence": "GSPGIRVL\r\nVLRRMHRPRSCSYQLLLEHQRPSCIQGLRWTPLTNSEESLDFSES\r\nLEQASTERVLRAGRQLHRHLLATCPNLIRDRKYHLRLYRQCCSGRELVDGILALGLGVHS\r\nRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQFYRFPGPEPEPVGTHEMEEELA\r\nEAVALLSQRGPDALLTVALRKPPGQRTDEELDLIFEELLHIKAVAHLSNSVKRELAAVLL\r\nFEPHSKAGTVLFSQGDKGTSWYIIWKGSVNVVTHGKGLVTTLHEGDDFGQLALVNDAPRA\r\nATIILREDNCHFLRVDKQDFNRIIKDVEAKTMRLEEHGKVVLVLERASQGAGPSRPPTP\r\nGRNRYTVMSGTPEKILELLLEAMGPDSSAHDPTETFLSDFLLTHRVFMPSAQLCAALLHH\r\nFHVEPAGGSEQERSTYVCNKRQQILRLVSQWVALYGSMLHTDPVATSFLQKLSDLVGRDT\r\nRLSNLLREQWPERRRCHRLENGCGNASPQMKARNLPVWLPNQDEPLPGSSCAIQVGDKVP\r\nYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQVLVKVNSAGDAIGLQPDARGVA\r\nTSLGLNERLFVVNPQEVHELIPHPDQLGPTVGSAEGLDLVSAKDLAGQLTDHDWSLFNSI\r\nHQVELIHYVLGPQHLRDVTTANLERFMRRFNELQYWVATELCLCPVPGPRAQLLRKFIKL\r\nAAHLKEQKNLNSFFAVMFGLSNSAISRLAHTWERLPHKVRKLYSALERLLDPSWNHRVYR\r\nLALAKLSPPVIPFMPLLLKDMTFIHEGNHTLVENLINFEKMRMMARAARMLHHCRSHNPV\r\nPLSPLRSRVSHLHEDSQVARISTCSEQSLSTRSPASTWAYVQQLKVIDNQRELSRLSREL\r\nEP",
"organism": "Homo sapiens",
"uniprot_code": "O95398",
"uniprot_range_first": 2,
"uniprot_range_last": 881,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLL\nEHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRK\nYHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQ\nFYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKPPGQRTDEELDLIFEEL\nLHIKAVAHLSNSVKRELAAVLLFEPHSKAGTVLFSQGDKGTSWYIIWKGSVNVVTHGKGL\nVTTLHEGDDFGQLALVNDAPRAATIILREDNCHFLRVDKQDFNRIIKDVEAKTMRLEEHG\nKVVLVLERASQGAGPSRPPTPGRNRYTVMSGTPEKILELLLEAMGPDSSAHDPTETFLSD\nFLLTHRVFMPSAQLCAALLHHFHVEPAGGSEQERSTYVCNKRQQILRLVSQWVALYGSML\nHTDPVATSFLQKLSDLVGRDTRLSNLLREQWPERRRCHRLENGCGNASPQMKARNLPVWL\nPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQV\nLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHPDQLGPTVGSAEGLDL\nVSAKDLAGQLTDHDWSLFNSIHQVELIHYVLGPQHLRDVTTANLERFMRRFNELQYWVAT\nELCLCPVPGPRAQLLRKFIKLAAHLKEQKNLNSFFAVMFGLSNSAISRLAHTWERLPHKV\nRKLYSALERLLDPSWNHRVYRLALAKLSPPVIPFMPLLLKDMTFIHEGNHTLVENLINFE\nKMRMMARAARMLHHCRSHNPVPLSPLRSRVSHLHEDSQVARISTCSEQSLSTRSPASTWA\nYVQQLKVIDNQRELSRLSRELEP",
"mw": 100.001,
"total_mw": 100.001,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "RAS related protein 1b",
"short_name": "Rap1b",
"sequence": "MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG\r\nTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL\r\nEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR",
"organism": "Mus musculus",
"uniprot_code": "Q52L50",
"uniprot_range_first": 1,
"uniprot_range_last": 167,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG\nTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL\nEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSS\nCQLL",
"mw": 18.0,
"total_mw": 18.0,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "1mM EDTA, 10mM DTT, 500mM NaCl, 1mM cAMP, and 10mM Tris",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 9.0,
"deuteration": null
},
"purity_method": null,
"name": "Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Texas, USA",
"full_name": "University of Texas Medical Branch",
"webpage": "http://www.bmb.utmb.edu/"
}
],
"contributor_name": "Mark",
"contributor_surname": "White",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-04-01",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1800.0,
"number_of_frames": 5,
"wavelength": 0.15418,
"sample_detector_distance": 0.489,
"concentration_min": 1.0,
"concentration_max": 4.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.123,
"s_max": 6.788,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCS6_fit1_model1_img.png",
"software": "SwissModel",
"pdb_link": [
{
"pdb_code": "3cf6",
"ext_code": "3CF6",
"ext_type": "pdb",
"difference_with_model": "other"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCS6_fit1_model1.pdb",
"model_mw": 119.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Combined remodelled 3CF6 with 4F7Z and SwissModel",
"user": 85
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCS6_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 0.9,
"p_value": 0.0228,
"fit_residual_plot": "SASDCS6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCS6_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CLcE4b.log",
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCS6_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCS6_fit2_model1.pdb",
"model_mw": 120.297,
"bead_radius": 3.75,
"log": null,
"symmetry": "P1",
"comment": "SAXNS_DAMMIF",
"user": 85
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCS6_fit2_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.767,
"p_value": 0.008,
"fit_residual_plot": "SASDCS6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCS6_fit2.fir",
"fit_log": null,
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SAXS data from solutions of Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP - in 1mM EDTA, 10mM DTT, 500mM NaCl, 1mM cAMP, 10mM Tris, pH 9 were collected using a Rigaku BioSAXS-1000 instrument at the Sealy Center For Structural Biology, UTMB-G (Galveston, TX, USA) equipped with a Kratky-2D Rigaku BioSAXS-1000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 4 mg/ml were measured at 10°C. SAXS data were acquired from 5 successive 1800 second frames. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration to generate the data displayed for this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 119.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 124.0,
"porod_mw_error": null,
"pddf_i0": 87670.0,
"pddf_i0_error": 763.0,
"guinier_i0": 85780.0,
"guinier_i0_error": 1523.0,
"pddf_rg": 4.27,
"pddf_rg_error": 0.03,
"guinier_rg": 4.05,
"guinier_rg_error": 0.09,
"pddf_dmax": 14.2,
"pddf_dmax_error": null,
"porod_volume": 207.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 14,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCS6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-07-03T15:06:29.480452+02:00",
"bragg_peak": []
}
