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{
"code": "SASDAA6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
"publication": {
"title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
"author_list": "Franke D, Jeffries CM, Svergun DI",
"journal": "Nat Methods",
"doi": "10.1038/nmeth.3358",
"pmid": "25849637",
"published_date": "2015 May"
},
"status": "released",
"submitted_date": null,
"released_date": "2015-05-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAA6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAA6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAA6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAA6.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": "Human serum albumin monomer",
"short_name": "HSA",
"sequence": "DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATL\r\nRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKR\r\nYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTK\r\nVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYA\r\nEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGE\r\nYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTES\r\nLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCK\r\nADDKETCFAEEGKKLVAASQAALGL",
"organism": "Homo sapiens",
"uniprot_code": "P02768",
"uniprot_range_first": 25,
"uniprot_range_last": 609,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\nEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\nERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\nFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\nARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\nECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\nRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\nQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\nLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\nSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\nAASQAALGL",
"mw": 66.47,
"total_mw": 66.47,
"number_molecules": 1,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES",
"concentration_unit": "mM",
"comment": null,
"additive": null,
"concentration": 50.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": "Size exclusion chromatography",
"name": "Human serum albumin monomer and mixtures",
"ext_coefficient": 0.518,
"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": "Daniel",
"contributor_surname": "Franke",
"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": "2014-01-22",
"storage_temperature": 20.0,
"cell_temperature": null,
"exposure_time": null,
"number_of_frames": null,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.16,
"s_max": 3.3,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAA6_fit1_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/SASDAA6_fit1_model1.pdb",
"model_mw": null,
"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/SASDAA6_fit1_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.075278,
"p_value": 0.3056,
"fit_residual_plot": "SASDAA6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit1.fir",
"fit_log": null,
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},
{
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{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAA6_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1e78",
"ext_code": "1e78",
"ext_type": "pdb",
"difference_with_model": null
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAA6_fit2_model1.pdb",
"model_mw": 61.91,
"bead_radius": 0.0,
"log": null,
"symmetry": "",
"comment": "ChainA from PDB 1E78",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAA6_fit2_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.01,
"p_value": 0.036,
"fit_residual_plot": "fit4columns145_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit2.fit",
"fit_log": null,
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},
{
"models": [
{
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"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1e78",
"ext_code": "1e78",
"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/SASDAA6_fit3_model1.pdb",
"model_mw": 60.85,
"bead_radius": 0.0,
"log": null,
"symmetry": "",
"comment": "ChainB from PDB 1E78",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAA6_fit3_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.0,
"p_value": 0.036,
"fit_residual_plot": "fit4columns146_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit3.fit",
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},
{
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"software": null,
"chi_square_value": 1.989,
"p_value": 0.0,
"fit_residual_plot": "SASDAA6_fit4_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit4.fit",
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},
{
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"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAA6_fit5_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.267,
"p_value": 0.0,
"fit_residual_plot": "SASDAA6_fit5_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit5.fit",
"fit_log": null,
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},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAA6_fit6_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.431,
"p_value": 0.0,
"fit_residual_plot": "SASDAA6_fit6_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA6_fit6.fit",
"fit_log": null,
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}
],
"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 from solutions of Human serum albumin in 50 mM HEPES, pH 7.5 were collected on the P12 beam line at Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle and λ = 0.12 nm). SAXS data of the HSA monomer were obtained from averaging 38 x 1 second frames spanning a separated HSA monomer elution peak from in-line size exclusion chromatography-SAXS (top four profiles and the respective ab initio and atomic model fits). The bottom three profiles are derived from un-purified stock solutions of HSA, consisting of monomers, dimers, and higher oligomeric species at three concentrations: 20 mg/ml, 10 mg/ml and 5 mg/ml. These data are included to illustrate the effects of repulsive interparticle interactions. The atomic model monomer fits to the HSA mixtures (using PDB 1E78_chain_A) are also shown, with chi2 values of 1.99 (20 mg/ml), 1.27 (10 mg/ml) and 1.43 (5 mg/ml). The p-value determined using Correlation map for the monomer fit to the mixture data is 0 in all instances, indicating statistically significant differences are present between the model and data (cf. a chi2 of 1.01 and p-value of 0.035 for the purified monomer model fit to the SEC-SAXS data).",
"tags": [
"benchmark"
],
"intensity_unit": null,
"experimental_mw": 61.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 61.0,
"porod_mw_error": null,
"pddf_i0": 522.8,
"pddf_i0_error": null,
"guinier_i0": 521.4,
"guinier_i0_error": null,
"pddf_rg": 2.8,
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"guinier_rg": 2.8,
"guinier_rg_error": null,
"pddf_dmax": 8.42,
"pddf_dmax_error": null,
"porod_volume": 103.43,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 117,
"pddf_point_first": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDAA6_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
