{"code":"SASDVD6","status":"Published","type_of_curve":"Merged","angular_unit":"1/A","project":{"title":"Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.","publication":{"title":"Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.","author_list":"Sargent R, Liu DH, Yadav R, Glennenmeier D, Bradford C, Urbina N, Beck MR","journal":"Protein Sci","doi":"10.1002/pro.70122","pmid":"40248864","published_date":"2025 May"},"status":"released","submitted_date":"2024-08-22","released_date":"2024-08-29"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVD6.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVD6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVD6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVD6.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Rayonix MX225-HE","resolution":null},"name":"Stanford Synchrotron Radiation Lightsource (SSRL)","city":"Menlo Park, CA","country":"USA","beamline_name":"BL4-2","beam_geometry":null,"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":"Palladin","short_name":"Ig4WT","sequence":"TVQERFFRPHFLQAPGDLTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPIRPDSAHKMLVRENGVHSLIIEPVTSRDAGIYTCIATNRAGQNSFNLELVVAAKEAHK","organism":"Mus musculus","uniprot_code":"Q9ET54","uniprot_range_first":1154,"uniprot_range_last":1257,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSETSSHDSFYDSLSDVQEEGKSADFFPGLSAFLSQEEINKSLDLARRAIDSSETEDFDS\nEKEISQIFSKSPISLCETPSHEEPKSGKQTSSERPQDSRRAPVQPLTGDQAERITSPGSK\nRKPGVSPLLASPSYIRSLRKAEKRGAKNPNPSSKPKTAQQSKAGPQSQLCDKAASFIEEL\nTSIFREAAKPRNRSPNGESSSPDSGYLSPKNQPSALMSASASQSPTADQLDQLEMDAEVK\nQAQGSLCYQAHQASEETLPLAHIPHPQPQKARHLPTAPRFIQKLRSQEVAEGSRVYLECR\nVTGNPTPRVRWFCEGKELYNSPDVQIHCESGELHTLVIAEAFEDDTGRYTCLATNPSGSD\nSTSAEVFIEGASSTDSDSESLSFISKAGAMPQAQKKTTSVSLTIGSSAPKTGVTTAVIQP\nLSVPVQQAHSATSYLCRPDGTTMGCLLPVFTKELQNTAASEGQVVVLECRVRGAPPLQVQ\nWFRQGSEIQDSPDFRILQKKPRSTAEPEEICTLVIAESFPEDAGIFTCSATNDYGSVTST\nAQLVITSANNENCSYDSTGEPNSDHFQHFPPPPPILETGSYELASQKPSEIQQVNSPNLG\nFSMAALQMQFNTAERETNGVHPSHGVNGLINGKAYGNKSPPTPTALLSPTKEPPPLLAKP\nKLDPLKLQQLQNQVRLEQEACAWPPAPPGVPCNSSSSGSSAPPSPPFPPPPPAFPELAAC\nASPVPSEPMSALASRATAMQSSGSFNYARPKQFIAAQNLGPASGLPTPTSSPSSSSLPSP\nLSPTPRPFGRAPGPPFVEPEAMWGPSSPSPPPPPPPVFSPSAAYPVPDVFPLPPPPPPLP\nSSTSHCASPARFGPSQTPAAFLSALLPSQPPPVAVNALGLPKGVTPAGFPKKSSRTARIA\nSDEEIQGTKDAVIQDLERKLRFKEDLLNNGQPRLTYEERMARRLLGADSANVFNIQEPEE\nTAANQDAGAPRASVGGPLDGQKEYKVSSCEQRLISEIEYRLERSPVDESGDEVQDPDVPV\nENATAPFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQRDLD\nGTCSLHTTASTLDDDGNYTIMAANPQGRVSCTGRLMVQAVNQRGRSPRSPSGHPHARRPR\nSRSRDSGDENEPIQERFFRPHFLQAPGDLTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPI\nRPDSAHKMLVRENGVHSLIIEPVTSRDAGIYTCIATNRAGQNSFNLELVVAAKEAHKAPV\nFMEKLQNTGVADGYPVRLECRVSGVPPPQIFWKKENESLTHSTERVSMHQDNHGYICLLI\nQGATKEDAGWYTVSAKNEAGIVSCTARLDVYTQWHQQPQTTKPKKVRPSASRYAALSDQG\nLDIKAAFQPEASPSHLTLNSGLVESEDL","mw":11.768,"total_mw":11.768,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains two additional non-native amino acids at the N-terminus (TV). The protein fragment encompasses the Ig-like C2-type 4 domain (Ig4WT)."}],"buffer":{"name":"20 mM HEPES pH 7.4, 1 mM DTT, 100 mM NaCl","concentration_unit":null,"comment":"HEPES storage buffer","additive":null,"concentration":null,"pka":null,"ph":null,"deuteration":null},"purity_method":null,"name":"The Ig-like C2-type 4 domain (Ig4WT) of Palladin","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":null,"full_name":"Wichita State University","webpage":null}],"contributor_name":"Rachel","contributor_surname":"Sargent","orcid":""}],"concentration_method":null,"concentration_unit":null,"date":"2023-08-29","storage_temperature":4.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":12,"wavelength":0.113,"sample_detector_distance":1.246,"concentration_min":0.5,"concentration_max":10.0,"sample_volume":null,"flow_rate":null,"s_min":0.104,"s_max":7.383,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVD6_fit1_model1_img.png","software":"SASREF","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":"2.8.2","model_data":"https://www.sasbdb.org/media/pdb_file/SASDVD6_fit1_model1.pdb","model_mw":10.78,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/4WTsasref.log","symmetry":null,"comment":null,"user":1106}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVD6_fit1_fixed_fit_img.png","software":"SASREF","chi_square_value":13.52,"p_value":0.0,"fit_residual_plot":"SASDVD6_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVD6_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/4WTsasref.log","software_version":"2.8.2","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVD6_fit2_model1_img.png","software":"SASREF","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVD6_fit2_model1.pdb","model_mw":10.78,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1106}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVD6_fit2_fixed_fit_img.png","software":"FoXS","chi_square_value":10.603084,"p_value":0.0,"fit_residual_plot":"SASDVD6_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVD6_fit2.fit","fit_log":null,"software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"NOTE: Amino acid sequence discrepancies are noted between on aligning the model and the submitted amino acid sequence.","experiment_description":"Synchrotron SAXS data from solutions of the Ig-like C2-type 4 domain (Ig4WT) of palladin in 20 mM HEPES pH 7.4, 1 mM DTT, 100 mM NaCl were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Menlo Park, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.2 m and at a wavelength of λ = 0.113 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 10 mg/ml were measured at 20°C. 12 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.","tags":[],"intensity_unit":"arbitrary","experimental_mw":10.2,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":11.3,"porod_mw_error":null,"pddf_i0":0.003862,"pddf_i0_error":null,"guinier_i0":0.00382275,"guinier_i0_error":null,"pddf_rg":1.77,"pddf_rg_error":null,"guinier_rg":1.691,"guinier_rg_error":0.082,"pddf_dmax":6.78,"pddf_dmax_error":null,"porod_volume":18.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":10,"guinier_point_last":87,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVD6_datloglog_img.png","symmetry":null,"last_modified":"2025-04-28T15:41:13.044270+02:00","bragg_peak":[]}