{ "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": [] }