{ "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": 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"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, "software_version": null, "description": null }, { "models": [ { "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, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAA6_fit3_model1_img.png", "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", "fit_log": null, "software_version": null, "description": null }, { "models": [], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAA6_fit4_fixed_fit_img.png", "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", "fit_log": null, "software_version": null, "description": null }, { "models": [], "fit_unit": "1/A", "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, "software_version": null, "description": null }, { "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, "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 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, "pddf_rg_error": null, "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, "pddf_point_last": null, "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": [] }