{ "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": [] }