{"code":"SASDES5","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Structural characterization of the third scavenger receptor cysteine-rich domain of murine neurotrypsin.","publication":{"title":"Structural characterization of the third scavenger receptor cysteine-rich domain of murine neurotrypsin.","author_list":"Canciani A, Catucci G, Forneris F","journal":"Protein Sci","doi":"10.1002/pro.3587","pmid":"30748049","published_date":"2019 Apr"},"status":"released","submitted_date":"2018-10-03","released_date":"2019-02-13"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDES5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDES5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDES5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDES5.sascif","experiment":{"instrument":{"detector":{"type":"Dectris","name":"Pilatus 1M","resolution":172.0},"name":"ESRF","city":"Grenoble","country":"France","beamline_name":"BM29","beam_geometry":"","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":"Mouse Neurotrypsin Scavenger Receptor Cysteine-Rich Domain 3","short_name":"mmNT-SRCR3","sequence":"GTGEFTSGSGFPIRLVDGENKKEGRVEVFVNGQWGTICDDGWTDKHAAVICRQLGYKGPARARTMAYFGEGKGPIHMDNVKCTGNEKALADCVKQDIGRHNCRHSEDAGVICDYLEKKASS","organism":"Mus musculus","uniprot_code":"O08762","uniprot_range_first":383,"uniprot_range_last":494,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MALARCVLAVILGALSVVARADPVSRSPLHRPHPSPPRSQHAHYLPSSRRPPRTPRFPLP\nLRIPAAQRPQVLSTGHTPPTIPRRCGAGESWGNATNLGVPCLHWDEVPPFLERSPPASWA\nELRGQPHNFCRSPDGSGRPWCFYRNAQGKVDWGYCDCGQGPALPVIRLVGGNSGHEGRVE\nLYHAGQWGTICDDQWDNADADVICRQLGLSGIAKAWHQAHFGEGSGPILLDEVRCTGNEL\nSIEQCPKSSWGEHNCGHKEDAGVSCVPLTDGVIRLAGGKSTHEGRLEVYYKGQWGTVCDD\nGWTEMNTYVACRLLGFKYGKQSSVNHFDGSNRPIWLDDVSCSGKEVSFIQCSRRQWGRHD\nCSHREDVGLTCYPDSDGHRLSPGFPIRLVDGENKKEGRVEVFVNGQWGTICDDGWTDKHA\nAVICRQLGYKGPARARTMAYFGEGKGPIHMDNVKCTGNEKALADCVKQDIGRHNCRHSED\nAGVICDYLEKKASSSGNKEMLSSGCGLRLLHRRQKRIIGGNNSLRGAWPWQASLRLRSAH\nGDGRLLCGATLLSSCWVLTAAHCFKRYGNNSRSYAVRVGDYHTLVPEEFEQEIGVQQIVI\nHRNYRPDRSDYDIALVRLQGPGEQCARLSTHVLPACLPLWRERPQKTASNCHITGWGDTG\nRAYSRTLQQAAVPLLPKRFCKERYKGLFTGRMLCAGNLQEDNRVDSCQGDSGGPLMCEKP\nDESWVVYGVTSWGYGCGVKDTPGVYTRVPAFVPWIKSVTSL","mw":13.165,"total_mw":13.165,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"25 mM HEPES, 0.1 M NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Neurotrypsin Scavenger Receptor Cysteine-Rich Domain 3 (mmNT-SRCR3) - from SEC-SAXS","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Italy","full_name":"University of Pavia","webpage":"http://wcm-3.unipv.it"}],"contributor_name":"Federico","contributor_surname":"Forneris","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-05-20","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":22,"wavelength":0.09919,"sample_detector_distance":2.87,"concentration_min":null,"concentration_max":15.0,"sample_volume":null,"flow_rate":null,"s_min":0.033,"s_max":4.944,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDES5_fit1_model1_img.png","software":"PDB (Protein Data Bank)","pdb_link":[{"pdb_code":"6h8m","ext_code":"6H8M","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/SASDES5_fit1_model1.pdb","model_mw":11.82,"bead_radius":null,"log":null,"symmetry":null,"comment":"Model generated from PDB file by selecting only chain A","user":294}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/A00_fit_img.png","software":"CRYSOL","chi_square_value":1.399,"p_value":0.0,"fit_residual_plot":null,"fit_data":"https://www.sasbdb.org/media/fitting_files/SASDES5_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/A00.log","software_version":"2.8.3","description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"2.8.4","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, 2θ is the scattering angle and λ the X-ray wavelength), were collected from a sample of mmNT-SRCR3 using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line of the ESRF (Grenoble France) coupled to a Nexera High Pressure Liquid/Chromatography (HPLC; Shimadzu) system. Data were collected using a Pilatus 1M detector at a sample-detector distance of 2.87 m (s-range; 0.03–4.5 nm-1) at a wavelength of λ = 0.09919 nm (12.5 keV). The SEC mobile phase consisted of 25 mM HEPES/NaOH, 0.1 M NaCl, pH 8, (20°C). The protein was concentrated to 15 mg/mL and a 15 µL of sample was run on a Superdex 75 Increase 3.2/300 column (GE Healthcare). Analysis and of the scattering intensities measured from the SEC-elution sample peak (22 successive 1 s frames) and the subtraction of intensities measured from an appropriate solvent-blank were was performed using CHROMIXS of the ATSAS suite. Comparison of in-solution scattering to crystallographic data was carried out with CRYSOL.","tags":[],"intensity_unit":"arbitrary","experimental_mw":12.0,"experimental_mw_error":null,"guinier_i0_mw":11.99,"guinier_i0_mw_error":1.0,"porod_mw":11.5,"porod_mw_error":null,"pddf_i0":13.45,"pddf_i0_error":0.019,"guinier_i0":13.48,"guinier_i0_error":0.015,"pddf_rg":1.53,"pddf_rg_error":0.003,"guinier_rg":1.54,"guinier_rg_error":0.03,"pddf_dmax":4.54,"pddf_dmax_error":0.02,"porod_volume":23.85,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":27,"guinier_point_last":173,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDES5_datloglog_img.png","symmetry":null,"last_modified":"2024-06-23T13:31:55.412859+02:00","bragg_peak":[]}