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": "SASDBJ3",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/nm",
"project": {
"title": "Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.",
"publication": {
"title": "Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.",
"author_list": "Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI",
"journal": "Nat Protoc",
"doi": "10.1038/nprot.2016.113",
"pmid": "27711050",
"published_date": "2016 Nov"
},
"status": "released",
"submitted_date": "2016-01-25",
"released_date": "2016-07-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBJ3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBJ3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBJ3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBJ3.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": "Bovine serum albumin, monomer",
"short_name": "BSA monomer",
"sequence": "DTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFA\r\nKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNE\r\nCFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYA\r\nPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLTSSARQRLRCA\r\nSIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLL\r\nECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPEN\r\nLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAK\r\nEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEY\r\nGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTED\r\nYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKA\r\nFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENF\r\nVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA",
"organism": "Bos taurus",
"uniprot_code": "P02769",
"uniprot_range_first": 25,
"uniprot_range_last": 607,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPF\nDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEP\nERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYY\nANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVA\nRLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE\nCCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRR\nHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK\nLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL\nNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLP\nDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV\nSTQTALA",
"mw": 66.462,
"total_mw": 66.462,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM Tris 150 mM NaCl 3% (v/v) glycerol",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl 3% v/v glycerol",
"concentration": 25.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Bovine serum albumin, monomer from SEC-SAXS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Clement",
"contributor_surname": "Blanchet",
"orcid": null
},
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Melissa ",
"contributor_surname": "Graewert",
"orcid": null
},
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
},
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Dmitri",
"contributor_surname": "Svergun",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-01-23",
"storage_temperature": 20.0,
"cell_temperature": null,
"exposure_time": 1.0,
"number_of_frames": 3500,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.086,
"s_max": 4.23,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBJ3_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "4f5s",
"ext_code": "4F5S",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBJ3_fit1_model1.pdb",
"model_mw": 66.44,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBJ3_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.11,
"p_value": 0.955951,
"fit_residual_plot": "SASDBJ3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBJ3_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBJ3_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBJ3_fit2_model1.pdb",
"model_mw": 41.658,
"bead_radius": 2.5,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBJ3_fit2_fit_img.png",
"software": null,
"chi_square_value": 0.972,
"p_value": 0.173,
"fit_residual_plot": "SASDBJ3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBJ3_fit2.fir",
"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": null,
"experiment_description": "X-ray synchrotron radiation scattering data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle) were collected from a sample of bovine serum albumin using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) in combination with RALLS/RI/UV measurements at the EMBL-P12 bioSAXS beam line on the Petra-III storage ring (Hamburg, Germany). The BSA sample (60 microlitres at 11.4 mg/ml) in 25 mM Tris 150 mM NaCl 3% v/v glycerol, pH 7.5 was injected onto a GE Healthcare S200 Increase 10/300 (24 ml) column at a flow rate of 0.4 ml/min. A total of 3600 x 1 second SAXS data frames were recorded throughout the BSA elution. After background solvent corrections, SEC-SAXS data frames 1411-1437, corresponding to monomeric BSA, were scaled and averaged to produce the data displayed in this entry. Additional files, including plots of I(0) and Rg vs frame number (determined by AUTORG) as well as the processed RALLS/RI molecular weight correlations are included in the additional files of the full entry zip archive.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 66.7,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 62.6,
"porod_mw_error": null,
"pddf_i0": 559.0,
"pddf_i0_error": 0.9,
"guinier_i0": 555.0,
"guinier_i0_error": 1.26,
"pddf_rg": 2.8,
"pddf_rg_error": null,
"guinier_rg": 2.77,
"guinier_rg_error": null,
"pddf_dmax": 8.23,
"pddf_dmax_error": null,
"porod_volume": 100.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 146,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBJ3_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
