The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDBE4",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "The Structure of the Plakin Domain of Plectin Reveals an Extended Rod-like Shape.",
"publication": {
"title": "The Structure of the Plakin Domain of Plectin Reveals an Extended Rod-like Shape.",
"author_list": "Ortega E, Manso JA, Buey RM, Carballido AM, Carabias A, Sonnenberg A, de Pereda JM",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.M116.732909",
"pmid": "27413182",
"published_date": "2016 Sep 2"
},
"status": "released",
"submitted_date": "2016-07-14",
"released_date": "2016-07-14"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBE4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBE4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBE4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBE4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBE4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBE4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBE4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "Plakin domain of Human Desmoplakin",
"short_name": "Desmoplakin",
"sequence": "GSHMWDEFTKHVTSECLGWMRQQRAEMDMVAWGVDLASVEQHINSHRGIHNSIGDYRWQL\r\nDKIKADLREKSAIYQLEEEYENLLKASFERMDHLRQLQNIIQATSREIMWINDCEEEELL\r\nYDWSDKNTNIAQKQEAFSIRMSQLEVKEKELNKLKQESDQLVLNQHPASDKIEAYMDTLQ\r\nTQWSWILQITKCIDVHLKENAAYFQFFEEAQSTEAYLKGLQDSIRKKYPCDKNMPLQHLL\r\nEQIKELEKEREKILEYKRQVQNLVNKSKKIVQLKPRNPDYRSNKPIILRALCDYKQDQKI\r\nVHKGDECILKDNNERSKWYVTGPGGVDMLVPSVGLIIPPPNPLAVDLSCKIEQYYEAILA\r\nLWNQLYINMKSLVSWHYCMIDIEKIRAMTIAKLKTMRQEDYMKTIADLELHYQEFIRNSQ\r\nGSEMFGDDDKRKIQSQFTDAQKHYQTLVIQLPGYPQHQTVTTTEITHHGTCQDVNHNKVI\r\nETNRENDKQETWMLMELQKIRRQIEHCEGRMTLKNLPLADQGSSHHITVKINELKSVQND\r\nSQAIAEVLNQLKDMLANFRGSEKYCYLQNEVFGLFQKLENINGVTDGYLNSLCTVRALLQ\r\nAILQTEDMLKVYEARLTEEETVCLDLDKVEAYRCGLKKIKNDLNLKKSLLATMKTELQKA\r\nQQIHSQTSQQYPLYDLDLGKFGEKVTQLTDRWQRIDKQIDFRLWDLEKQIKQLRNYRDNY\r\nQAFCKWLYDAKRRQDSLESMKFGDSNTVMRFLNEQKNLHSEISGKRDKSEEVQKIAELCA\r\nNSIKDYELQLASYTSGLETLLNIPIKRTMIQSPSGVILQEAADVHARYIELLTRSGDYYR",
"organism": "Homo sapiens",
"uniprot_code": "P15924",
"uniprot_range_first": 180,
"uniprot_range_last": 1025,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSCNGGSHPRINTLGRMIRAESGPDLRYEVTSGGGGTSRMYYSRRGVITDQNSDGYCQTG\nTMSRHQNQNTIQELLQNCSDCLMRAELIVQPELKYGDGIQLTRSRELDECFAQANDQMEI\nLDSLIREMRQMGQPCDAYQKRLLQLQEQMRALYKAISVPRVRRASSKGGGGYTCQSGSGW\nDEFTKHVTSECLGWMRQQRAEMDMVAWGVDLASVEQHINSHRGIHNSIGDYRWQLDKIKA\nDLREKSAIYQLEEEYENLLKASFERMDHLRQLQNIIQATSREIMWINDCEEEELLYDWSD\nKNTNIAQKQEAFSIRMSQLEVKEKELNKLKQESDQLVLNQHPASDKIEAYMDTLQTQWSW\nILQITKCIDVHLKENAAYFQFFEEAQSTEAYLKGLQDSIRKKYPCDKNMPLQHLLEQIKE\nLEKEREKILEYKRQVQNLVNKSKKIVQLKPRNPDYRSNKPIILRALCDYKQDQKIVHKGD\nECILKDNNERSKWYVTGPGGVDMLVPSVGLIIPPPNPLAVDLSCKIEQYYEAILALWNQL\nYINMKSLVSWHYCMIDIEKIRAMTIAKLKTMRQEDYMKTIADLELHYQEFIRNSQGSEMF\nGDDDKRKIQSQFTDAQKHYQTLVIQLPGYPQHQTVTTTEITHHGTCQDVNHNKVIETNRE\nNDKQETWMLMELQKIRRQIEHCEGRMTLKNLPLADQGSSHHITVKINELKSVQNDSQAIA\nEVLNQLKDMLANFRGSEKYCYLQNEVFGLFQKLENINGVTDGYLNSLCTVRALLQAILQT\nEDMLKVYEARLTEEETVCLDLDKVEAYRCGLKKIKNDLNLKKSLLATMKTELQKAQQIHS\nQTSQQYPLYDLDLGKFGEKVTQLTDRWQRIDKQIDFRLWDLEKQIKQLRNYRDNYQAFCK\nWLYDAKRRQDSLESMKFGDSNTVMRFLNEQKNLHSEISGKRDKSEEVQKIAELCANSIKD\nYELQLASYTSGLETLLNIPIKRTMIQSPSGVILQEAADVHARYIELLTRSGDYYRFLSEM\nLKSLEDLKLKNTKIEVLEEELRLARDANSENCNKNKFLDQNLQKYQAECSQFKAKLASLE\nELKRQAELDGKSAKQNLDKCYGQIKELNEKITRLTYEIEDEKRRRKSVEDRFDQQKNDYD\nQLQKARQCEKENLGWQKLESEKAIKEKEYEIERLRVLLQEEGTRKREYENELAKVRNHYN\nEEMSNLRNKYETEINITKTTIKEISMQKEDDSKNLRNQLDRLSRENRDLKDEIVRLNDSI\nLQATEQRRRAEENALQQKACGSEIMQKKQHLEIELKQVMQQRSEDNARHKQSLEEAAKTI\nQDKNKEIERLKAEFQEEAKRRWEYENELSKVRNNYDEEIISLKNQFETEINITKTTIHQL\nTMQKEEDTSGYRAQIDNLTRENRSLSEEIKRLKNTLTQTTENLRRVEEDIQQQKATGSEV\nSQRKQQLEVELRQVTQMRTEESVRYKQSLDDAAKTIQDKNKEIERLKQLIDKETNDRKCL\nEDENARLQRVQYDLQKANSSATETINKLKVQEQELTRLRIDYERVSQERTVKDQDITRFQ\nNSLKELQLQKQKVEEELNRLKRTASEDSCKRKKLEEELEGMRRSLKEQAIKITNLTQQLE\nQASIVKKRSEDDLRQQRDVLDGHLREKQRTQEELRRLSSEVEALRRQLLQEQESVKQAHL\nRNEHFQKAIEDKSRSLNESKIEIERLQSLTENLTKEHLMLEEELRNLRLEYDDLRRGRSE\nADSDKNATILELRSQLQISNNRTLELQGLINDLQRERENLRQEIEKFQKQALEASNRIQE\nSKNQCTQVVQERESLLVKIKVLEQDKARLQRLEDELNRAKSTLEAETRVKQRLECEKQQI\nQNDLNQWKTQYSRKEEAIRKIESEREKSEREKNSLRSEIERLQAEIKRIEERCRRKLEDS\nTRETQSQLETERSRYQREIDKLRQRPYGSHRETQTECEWTVDTSKLVFDGLRKKVTAMQL\nYECQLIDKTTLDKLLKGKKSVEEVASEIQPFLRGAGSIAGASASPKEKYSLVEAKRKKLI\nSPESTVMLLEAQAATGGIIDPHRNEKLTVDSAIARDLIDFDDRQQIYAAEKAITGFDDPF\nSGKTVSVSEAIKKNLIDRETGMRLLEAQIASGGVVDPVNSVFLPKDVALARGLIDRDLYR\nSLNDPRDSQKNFVDPVTKKKVSYVQLKERCRIEPHTGLLLLSVQKRSMSFQGIRQPVTVT\nELVDSGILRPSTVNELESGQISYDEVGERIKDFLQGSSCIAGIYNETTKQKLGIYEAMKI\nGLVRPGTALELLEAQAATGFIVDPVSNLRLPVEEAYKRGLVGIEFKEKLLSAERAVTGYN\nDPETGNIISLFQAMNKELIEKGHGIRLLEAQIATGGIIDPKESHRLPVDIAYKRGYFNEE\nLSEILSDPSDDTKGFFDPNTEENLTYLQLKERCIKDEETGLCLLPLKEKKKQVQTSQKNT\nLRKRRVVIVDPETNKEMSVQEAYKKGLIDYETFKELCEQECEWEEITITGSDGSTRVVLV\nDRKTGSQYDIQDAIDKGLVDRKFFDQYRSGSLSLTQFADMISLKNGVGTSSSMGSGVSDD\nVFSSSRHESVSKISTISSVRNLTIRSSSFSDTLEESSPIAAIFDTENLEKISITEGIERG\nIVDSITGQRLLEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGFEG\nVKGKKKMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEAIRKGFIDGRA\nAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGLRLLEAASVSSKGLPSPYNMS\nSAPGSRSGSRSGSRSGSRSGSRSGSRRGSFDATGNSSYSYSYSFSSSSIGH",
"mw": 98.68,
"total_mw": 98.68,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 3 mM DTT",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl, 5% glycerol, 3 mM DTT",
"concentration": 20.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Plakin domain of Human desmoplakin",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "USAL",
"address": "Salamanca, Spain",
"full_name": "La Universidad de Salamanca",
"webpage": "http://www.usal.es"
}
],
"contributor_name": "Jose M",
"contributor_surname": "de Pereda",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2015-09-25",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 30,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": 0.59,
"concentration_max": 4.7,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.062,
"s_max": 4.812,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBE4_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBE4_fit1_model1.pdb",
"model_mw": 99.44,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_007_1.log",
"symmetry": "",
"comment": "",
"user": 26
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBE4_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBE4_fit1_model2.pdb",
"model_mw": 99.44,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBE4_fit1_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBE4_fit1_model3.pdb",
"model_mw": 99.44,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBE4_fit1_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBE4_fit1_model4.pdb",
"model_mw": 99.44,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBE4_fit1_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBE4_fit1_model5.pdb",
"model_mw": 99.44,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBE4_fit1_fixed_fit_img.png",
"software": null,
"chi_square_value": 3.2,
"p_value": 4e-06,
"fit_residual_plot": "fit4columns429_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBE4_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The models displayed for this entry are selected representatives from a refined ensemble of conformations derived from ensemble optimization method (EOM). The Rg and Dmax distributions of the ensemble and the additional results from EOM (that includes additional structural representatives) are available in the full-entry zip archive. The corresponding fit for this entry shows the final EOM fit to the SAXS data of the total refined ensemble.",
"experiment_description": "Synchrotron SAXS data from solutions of the plakin domain from Human desmoplakin in 20 mM sodium phosphate, 150 mM NaCl, 5% v/v glycerol, 3 mM DTT were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 0.59-4.70 mg/ml were measured using an exposure time of 1.5 s (recorded as 30 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data were normalized to protein concentration and then extrapolated to infinite dilution to simulate a zero-concentration scattering curve.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 114.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 85.0,
"porod_mw_error": null,
"pddf_i0": 25920.0,
"pddf_i0_error": null,
"guinier_i0": 25300.0,
"guinier_i0_error": null,
"pddf_rg": 8.34,
"pddf_rg_error": null,
"guinier_rg": 7.49,
"guinier_rg_error": null,
"pddf_dmax": 35.0,
"pddf_dmax_error": null,
"porod_volume": 136.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": null,
"guinier_point_last": null,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBE4_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
