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{
"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": []
}
