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": "SASDAY7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Structure and target interaction of a G-quadruplex RNA-aptamer.",
"publication": {
"title": "Structure and target interaction of a G-quadruplex RNA-aptamer.",
"author_list": "Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U",
"journal": "RNA Biol",
"doi": "10.1080/15476286.2016.1212151",
"pmid": "27471797",
"published_date": "2016 Oct 2"
},
"status": "released",
"submitted_date": null,
"released_date": "2016-09-08"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAY7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAY7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAY7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAY7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAY7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAY7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAY7.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": "1 x 5 mm",
"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": "Interleukin-6 receptor subunit alpha",
"short_name": "IL-6R",
"sequence": "MRAWIFFLLCLAGRALAAPLVHHHHHHALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHWVLRKPAAGSHP\r\nSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVR\r\nKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNP\r\nRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPVQ",
"organism": "Homo sapiens",
"uniprot_code": "P08887",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MLAVGCALLAALLAAPGAALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHW\nVLRKPAAGSHPSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLS\nCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAV\nPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQD\nPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQ\nGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPVQDSS\nSVPLPTFLVAGGSLAFGTLLCIAIVLRFKKTWKLRALKEGKTSMHPPYSLGQLVPERPRP\nTPVLVPLISPPVSPSSLGSDNTSSHNRPDARDPRSPYDISNTDYFFPR",
"mw": 40.964,
"total_mw": 163.855,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Interleukin-6 receptor subunit alpha",
"short_name": "IL-6R",
"sequence": "MRAWIFFLLCLAGRALAAPLVHHHHHHALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHWVLRKPAAGSHP\r\nSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVR\r\nKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNP\r\nRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPVQ",
"organism": "Homo sapiens",
"uniprot_code": "P08887",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MLAVGCALLAALLAAPGAALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHW\nVLRKPAAGSHPSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLS\nCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAV\nPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQD\nPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQ\nGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPVQDSS\nSVPLPTFLVAGGSLAFGTLLCIAIVLRFKKTWKLRALKEGKTSMHPPYSLGQLVPERPRP\nTPVLVPLISPPVSPSSLGSDNTSSHNRPDARDPRSPYDISNTDYFFPR",
"mw": 40.964,
"total_mw": 81.928,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "water",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "IL-6R tetramer-dimer equilibrium",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"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": "Erica",
"contributor_surname": "Valentini",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2014-10-01",
"storage_temperature": null,
"cell_temperature": null,
"exposure_time": null,
"number_of_frames": null,
"wavelength": null,
"sample_detector_distance": 3.9,
"concentration_min": null,
"concentration_max": 0.1,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.026,
"s_max": 4.011,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAY7_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "1n26",
"ext_code": "1n26",
"ext_type": "pdb",
"difference_with_model": null
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAY7_fit1_model1.pdb",
"model_mw": 171.8,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 1
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAY7_fit1_fit_img.png",
"software": null,
"chi_square_value": 2.49,
"p_value": 0.0,
"fit_residual_plot": "SASDAY7_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAY7_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAY7_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAY7_fit2_model1.pdb",
"model_mw": 171.8,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 1
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAY7_fit2_model2_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAY7_fit2_model2.pdb",
"model_mw": 85.9,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "extended dimer",
"user": 1
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAY7_fit2_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 1.3,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAY7_fit2.fit",
"fit_log": null,
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAY7_fit3_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAY7_fit3_model1.pdb",
"model_mw": 171.8,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 1
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAY7_fit3_model2_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAY7_fit3_model2.pdb",
"model_mw": 84.8,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "compact dimer",
"user": 1
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAY7_fit3_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 1.92,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAY7_fit3.fit",
"fit_log": null,
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The curve was fitted with a tetramer obtained with CORAL from the unit cell tetrameric structure of the pdb code 1N26 with a Chi-squared-value of 2.49. Since the experimental MW appeared smaller than a tetramer (confirmed by a not-fitting tetrameric model) we tried to fit a mixture of tetramer-dimer using OLIGOMER. Two possible dimers were possible: a compact and an extended one. With the compact dimer mixture OLIGOMER estimated a volume fraction of 65% tetramer and 35% dimer and a corresponding Chi-squared-value of 1.92. With the extended dimer mixture OLIGOMER estimated a volume fraction of 47% tetramer and 53% dimer and a improved Chi-squared-value of 1.33.",
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 143.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 143.0,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 0.025,
"guinier_i0_error": null,
"pddf_rg": 5.1,
"pddf_rg_error": null,
"guinier_rg": 4.9,
"guinier_rg_error": null,
"pddf_dmax": 20.0,
"pddf_dmax_error": 2.0,
"porod_volume": 240.0,
"porod_volume_error": 40.0,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 17,
"guinier_point_last": 76,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDAY7_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
