{ "code": "SASDEE5", "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/SASDEE5.d", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEE5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEE5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEE5.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", "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 synchrotron 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": "2017-11-26", "storage_temperature": 10.0, "cell_temperature": 20.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 4.3, "sample_volume": null, "flow_rate": null, "s_min": 0.023, "s_max": 5.055, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEE5_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "4f52", "ext_code": "4F52", "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/SASDEE5_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/BSA_monomer_4f5s00_MwdDtgP_fit_img.png", "software": "CRYSOL", "chi_square_value": 13.337, "p_value": 0.0, "fit_residual_plot": "BSA_monomer_4f5s00_MwdDtgP_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEE5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BSA_monomer_4f5s00_PWscLoW.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEE5_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/SASDEE5_fit2_model1.pdb", "model_mw": 56.243, "bead_radius": 3.0, "log": null, "symmetry": "P1", "comment": null, "user": 365 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/RBS_A_BSAmon_P12_trunc_01_8e9iSXR_fit_img.png", "software": "DAMMIF", "chi_square_value": 3.967, "p_value": 5e-06, "fit_residual_plot": "RBS_A_BSAmon_P12_trunc_01_8e9iSXR_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEE5_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/RBS_A_BSAmon_P12_trunc_01_NNzpXxP.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "BayesApp", "pddf_software_version": null, "i0_calibration_standard": null, "description": "The data have been binned logarithmically and scaled to overlap with static in-house SAXS BSA data (SASDEB5).", "experiment_description": "Synchrotron SAXS data from solutions of Bovine serum albumin in 50 mM HEPES, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.30 mg/ml was measured at 20°C. 20 successive 0.050 second frames were 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": "arbitrary", "experimental_mw": 66.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 66.0, "porod_mw_error": null, "pddf_i0": 0.5731097, "pddf_i0_error": null, "guinier_i0": 0.045, "guinier_i0_error": 6.13e-05, "pddf_rg": 2.8, "pddf_rg_error": null, "guinier_rg": 2.766, "guinier_rg_error": 0.006, "pddf_dmax": 9.5, "pddf_dmax_error": null, "porod_volume": 85.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 51, "guinier_point_last": 81, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEE5_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }