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{
"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": []
}
