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{
"code": "SASDEB5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"publication": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"author_list": "Bucciarelli S, Midtgaard SR, Nors Pedersen M, Skou S, Arleth L, Vestergaard B",
"journal": "J Appl Crystallogr",
"doi": "10.1107/S1600576718014462",
"pmid": "30546289",
"published_date": "2018 Dec 1"
},
"status": "released",
"submitted_date": "2018-09-29",
"released_date": "2018-11-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEB5.d",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEB5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEB5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEB5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "pixel counting",
"name": "Pilatus3 R 300K",
"resolution": 172.0
},
"name": "University of Copenhagen, Department of Drug Design and Pharmacology",
"city": "Copenhagen",
"country": "Denmark",
"beamline_name": "Xenocs BioXolver L with MetalJet",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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",
"short_name": "BSA",
"sequence": "DTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFAKTCVADESHA\r\nGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPN\r\nTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPK\r\nIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKV\r\nHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPEN\r\nLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECC\r\nAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTP\r\nTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESL\r\nVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATE\r\nEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA",
"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": 66.432,
"total_mw": 66.432,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Bovine serum albumin from in-house SAXS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Copenhagen, Denmark",
"full_name": "University of Copenhagen",
"webpage": "http://www.ku.dk/"
}
],
"contributor_name": "Saskia",
"contributor_surname": "Bucciarelli",
"orcid": "https://orcid.org/0000-0001-7612-223X"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-05-04",
"storage_temperature": null,
"cell_temperature": 25.0,
"exposure_time": 60.0,
"number_of_frames": 1,
"wavelength": 0.134,
"sample_detector_distance": 0.654,
"concentration_min": null,
"concentration_max": 4.6,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.111,
"s_max": 4.48,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEB5_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": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEB5_fit1_model1.pdb",
"model_mw": 66.44,
"bead_radius": null,
"log": null,
"symmetry": "C1",
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/4f5s_BSAmonomer01_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.027,
"p_value": 0.007546,
"fit_residual_plot": "4f5s_BSAmonomer01_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEB5_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4f5s_BSAmonomer01.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEB5_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEB5_fit2_model1.pdb",
"model_mw": 64.335,
"bead_radius": 2.75,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/R_BSA_4p5_60s_not_c-norm_01_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.81,
"p_value": 0.322994,
"fit_residual_plot": "R_BSA_4p5_60s_not_c-norm_01_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEB5_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/R_BSA_4p5_60s_not_c-norm_01.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "BayesApp",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The background corrected data was binned logarithmically, normalized by concentration and brought to absolute scale using water as a secondary standard.",
"experiment_description": "SAXS data from solutions of Bovine serum albumin from in-house SAXS in 50 mM HEPES, pH 7.5 were collected on a Xenocs BioXolver L instrument at the Copenhagen University, Department of Drug Design and Pharmacology (Copenhagen, Denmark) using a 20Hz Pilatus 300K detector at a sample-detector distance of 0.7 m and at a wavelength of λ = 0.134 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.60 mg/ml was measured at 25°C. One 60 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 66.0,
"experimental_mw_error": null,
"guinier_i0_mw": 63.7,
"guinier_i0_mw_error": null,
"porod_mw": 66.0,
"porod_mw_error": null,
"pddf_i0": 0.5810089,
"pddf_i0_error": null,
"guinier_i0": 0.212,
"guinier_i0_error": 0.00208,
"pddf_rg": 2.84,
"pddf_rg_error": null,
"guinier_rg": 2.842,
"guinier_rg_error": 0.043,
"pddf_dmax": 9.42,
"pddf_dmax_error": null,
"porod_volume": 99.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 5,
"guinier_point_last": 28,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEB5_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
