{ "code": "SASDW23", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Cryo-EM led analysis of open and closed conformations of Chagas vaccine candidate TcPOP.", "publication": { "title": "Cryo-EM led analysis of open and closed conformations of Chagas vaccine candidate TcPOP.", "author_list": "Batra S, Olmo F, Ragan TJ, Kaplan M, Calvaresi V, Frank AM, Lancey C, Assadipapari M, Ying C, Struwe WB, Hesketh EL, Kelly JM, Barfod L, Campeotto I", "journal": "Nat Commun", "doi": "10.1038/s41467-025-62068-3", "pmid": "40764299", "published_date": "2025 Aug 5" }, "status": "released", "submitted_date": "2024-12-07", "released_date": "2025-08-07" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDW23.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW23.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW23_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW23_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW23_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW23_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW23.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger 4M", "resolution": 75.0 }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "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": "Prolyl endopeptidase", "short_name": null, "sequence": "MRSVYPLARRSMAAYTMHNMTVPEPYDYLEDPENPETKTFVNEQNAFFEEYFASEAELRKKIFESISNSQ\r\nDYPRTSNPSYINGHYYYYHNSGLQNQSVLMRAMSLTDTAPSIFLDPNSMSSDGTTALKATAWSEDESMLA\r\nYSLSDKGSDWQRIHVRRADTVEDTSDVIEWAKFTAIAWWHNLGFFYTRYPALQGDVDKGAETDAAQDAFI\r\nCFHRIGRPQDEDVVILSVPEHPQWNMGASVSDCHSYVIVVLFDGCEPHNLVWVAELPSVEKGLGSEPLVF\r\nKKLVNEFAGRYTYLGNEGSTFYFVTTRDAPRKKIVSIDIHTGQETVIVEQQRSVLSQAALVKKTLLLAYL\r\nEDVKDVFYYCRLEDPTLNAIPLPIGTITSFFSDRKKDFVSFKITSFLLPGRSFFLDINDPQSSLRVFKDD\r\nTVEGLLVDDFVTEQTFYNSSDGVRIPMFIVYRKGSVSSESPLLLYGYGGFNIPLTPAFSSSRMVFLRDLG\r\nGVLAVLNIRGGGEYGEEWHDAGRRACKQNCFTDFIEGAKFLHRQGYGSPQTTAIMGGSNGGLLVAAVANQ\r\nAPELFRCVVCRVGVLDMYKFHKFTIGHAWKSDYGDPEKEEDFRVLQQYSPLHNIKSGIKYPAILVVTGDH\r\nDDRVVPLHSLKYVATLQHMNPNEGGPFLARIEVAAGHGAGKPTSKILREAGDIYTFIAKNINASWKE", "organism": "Trypanosoma cruzi", "uniprot_code": "Q71MD6", "uniprot_range_first": 1, "uniprot_range_last": 697, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MRSVYPLARRSMAAYTMHNMTVPEPYDYLEDPENPETKTFVNEQNAFFEEYFASEAELRK\nKIFESISNSQDYPRTSNPSYINGHYYYYHNSGLQNQSVLMRAMSLTDTAPSIFLDPNSMS\nSDGTTALKATAWSEDESMLAYSLSDKGSDWQRIHVRRADTVEDTSDVIEWAKFTAIAWWH\nNLGFFYTRYPALQGDVDKGAETDAAQDAFICFHRIGRPQDEDVVILSVPEHPQWNMGASV\nSDCHSYVIVVLFDGCEPHNLVWVAELPSVEKGLGSEPLVFKKLVNEFAGRYTYLGNEGST\nFYFVTTRDAPRKKIVSIDIHTGQETVIVEQQRSVLSQAALVKKTLLLAYLEDVKDVFYYC\nRLEDPTLNAIPLPIGTITSFFSDRKKDFVSFKITSFLLPGRSFFLDINDPQSSLRVFKDD\nTVEGLLVDDFVTEQTFYNSSDGVRIPMFIVYRKGSVSSESPLLLYGYGGFNIPLTPAFSS\nSRMVFLRDLGGVLAVLNIRGGGEYGEEWHDAGRRACKQNCFTDFIEGAKFLHRQGYGSPQ\nTTAIMGGSNGGLLVAAVANQAPELFRCVVCRVGVLDMYKFHKFTIGHAWKSDYGDPEKEE\nDFRVLQQYSPLHNIKSGIKYPAILVVTGDHDDRVVPLHSLKYVATLQHMNPNEGGPFLAR\nIEVAAGHGAGKPTSKILREAGDIYTFIAKNINASWKE", "mw": 78.335, "total_mw": 78.335, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl", "concentration_unit": null, "comment": "Purification buffer", "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "SEC-SAXS of Trypanosoma cruzi Prolyl Oligopepetidase (TcPOP)", "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": "university of nottingham", "webpage": null } ], "contributor_name": "Ivan", "contributor_surname": "Campeotto", "orcid": "https://orcid.org/0000-0002-0814-619X" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-04-24", "storage_temperature": 15.0, "cell_temperature": 15.0, "exposure_time": 3.0, "number_of_frames": 600, "wavelength": 0.09464, "sample_detector_distance": 3.6856, "concentration_min": null, "concentration_max": 8.0, "sample_volume": 50.0, "flow_rate": 0.08, "s_min": 0.045, "s_max": 3.4, "total_exposure_time": null, "seccolumn": 2 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDW23_fit1_model1_img.png", "software": "AlphaFold", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDW23_fit1_model1.pdb", "model_mw": 78.31, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/open_jEX66Kv.log", "symmetry": "C1", "comment": null, "user": 1152 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW23_fit1_fixed_fit_img.png", "software": "DENSS", "chi_square_value": 1.0833, "p_value": 0.0064, "fit_residual_plot": "SASDW23_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDW23_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/avrg_001_16.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDW23_fit2_model1_img.png", "software": "AlphaFold", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDW23_fit2_model1.pdb", "model_mw": 78.31, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/close.log", "symmetry": "C1", "comment": null, "user": 1152 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW23_fit2_fixed_fit_img.png", "software": "DENSS", "chi_square_value": 1.0356, "p_value": 0.0002, "fit_residual_plot": "SASDW23_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDW23_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/avrg_001_9.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "BioXTAS RAW", "pddf_software_version": null, "i0_calibration_standard": null, "description": "CAUTION! Primary display data is different to the data used for modelling! CAUTION! Data used for modelling has NO GUINIER REGION, i.e., does not encompass the particle size/volume and radius of gyration! CAUTION! The models displayed in this entry were NOT used to calculate the fits to the data and therefore have no connection/relevance to the fits displayed in this entry (interpret model fits with extreme caution)!", "experiment_description": null, "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 78.5, "experimental_mw_error": null, "guinier_i0_mw": 75.0, "guinier_i0_mw_error": null, "porod_mw": 88.0, "porod_mw_error": null, "pddf_i0": 0.01530873, "pddf_i0_error": null, "guinier_i0": 0.0248482, "guinier_i0_error": null, "pddf_rg": 0.0, "pddf_rg_error": null, "guinier_rg": 3.0, "guinier_rg_error": 0.103, "pddf_dmax": 0.03, "pddf_dmax_error": null, "porod_volume": 142.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 45, "guinier_point_last": 298, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDW23_datloglog_img.png", "symmetry": null, "last_modified": "2025-08-07T13:57:51.099551+02:00", "bragg_peak": [] }