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{
"code": "SASDCJ3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"publication": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"author_list": "Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE",
"journal": "Acta Crystallogr D Struct Biol",
"doi": "10.1107/S2059798317011597",
"pmid": "28876235",
"published_date": "2017 Sep 1"
},
"status": "released",
"submitted_date": "2017-05-06",
"released_date": "2017-08-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCJ3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCJ3.dat",
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"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ3_kratky_img.png",
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"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCJ3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Australian Synchrotron",
"city": "Melbourne",
"country": "Australia",
"beamline_name": "SAXS/WAXS",
"beam_geometry": "Point",
"type_of_source": "X-ray synchrotron",
"point_source": true,
"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": "Serum albumin",
"short_name": null,
"sequence": "DTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA",
"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": "25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Bovine Serum Albumin",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Sydney, New South Wales 2006, Australia",
"full_name": "School of Molecular Bioscience, University of Sydney.",
"webpage": ""
}
],
"contributor_name": "Jill",
"contributor_surname": "Trewhella",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-03-09",
"storage_temperature": null,
"cell_temperature": 22.0,
"exposure_time": 1.0,
"number_of_frames": 24,
"wavelength": 0.10332,
"sample_detector_distance": 2.683,
"concentration_min": null,
"concentration_max": 0.56,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.066,
"s_max": 3.104,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
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"type_of_model": "dummy",
"software_version": "on-line",
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"model_mw": 57.74,
"bead_radius": 2.2,
"log": "https://www.sasbdb.org/media/log_files/3BSA.log",
"symmetry": "P1",
"comment": "",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ3_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.85,
"p_value": 0.156,
"fit_residual_plot": "SASDCJ3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCJ3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/3BSA.log",
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},
{
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"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCJ3_fit2_model1_img.png",
"software": "MultiFoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "on-line",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCJ3_fit2_model1.pdb",
"model_mw": 66.59,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Multi-FoXS 1-state model based on PDB:4F5S chain A with residues 187-183 & 381-384 flexible",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ3_fit2_fitfoxs_img.png",
"software": "MES-FoXS",
"chi_square_value": 1.05,
"p_value": 0.023,
"fit_residual_plot": "SASDCJ3_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCJ3_fit2.dat",
"fit_log": null,
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},
{
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"pdb_link": [
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"pdb_code": "4f5s",
"ext_code": "4F5S",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
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"log": null,
"symmetry": "P1",
"comment": "Multi-FoXS e1-0 3-state model based on PDB:4F5S chain A with residues 187-183 & 381-384 flexible",
"user": 138
},
{
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"log": null,
"symmetry": "P1",
"comment": "Multi-FoXS e1-1 3-state model based on PDB:4F5S chain A with residues 187-183 & 381-384 flexible",
"user": 138
},
{
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"log": null,
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"comment": "Multi-FoXS e1-2 3-state model based on PDB:4F5S chain A with residues 187-183 & 381-384 flexible",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ3_fit3_fitfoxs_img.png",
"software": "MES-FoXS",
"chi_square_value": 0.82,
"p_value": 0.1709,
"fit_residual_plot": "SASDCJ3_fit3_fitfoxsresiduals_img.png",
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "2.80",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of bovine serum albumin in 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3, pH 7.5 were collected on the SAXS/WAXS beam line at Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Scattering data are on an absolute scale (cm-1) set by reference to the scattering from pure H2O. I(0) values must be corrected for the shear flow sample cell by a 2.05 multiplicative factor. Data were acquired in SEC-SAXS mode, summed from 10 measurement frames where Rg was flat and at a maximum. The average concentration over the frames was 0.57 mg/mL, spanning values from 0.31 - 0.76 mg/mL. Sample concentrations were measured by A280 (extinction coefficient for 1 mg/mL, 10 mm pathlength; E0.1% = 0.646), corrected for the 3.1 mm path-length of the UV measurement cell. MULCh was used to calculate the partial specific volume (0.0.732 mL/g) and X-ray contrast (Δρ = 2.863e10 cm-2). The protein is a monmer in the solution conditions measured. The Multi-state (Multi-FoXS) fits to the data assumed flexible residues 183-187 and 381-384 in the loops that link the two tightly networked domains and proposed to be responsible for domain movements based upon their high temperature factors in the crystal structure.",
"tags": [
"benchmark"
],
"intensity_unit": "1/cm",
"experimental_mw": 66.43,
"experimental_mw_error": null,
"guinier_i0_mw": 65.12,
"guinier_i0_mw_error": null,
"porod_mw": 67.333,
"porod_mw_error": null,
"pddf_i0": 0.04249,
"pddf_i0_error": 3.4e-05,
"guinier_i0": 0.04245,
"guinier_i0_error": 4.2e-05,
"pddf_rg": 2.832,
"pddf_rg_error": 0.003,
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"pddf_dmax": 8.7,
"pddf_dmax_error": null,
"porod_volume": 101.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 51,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCJ3_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-03-03T13:31:13.115528+01:00",
"bragg_peak": []
}
