{ "code": "SASDED5", "status": "Published", "type_of_curve": "SEC-SAS", "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/SASDED5.d", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDED5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDED5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDED5.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "PBS + 1 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Bovine serum albumin monomer from synchrotron SEC-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": "2018-06-14", "storage_temperature": null, "cell_temperature": 10.0, "exposure_time": 1.0, "number_of_frames": 40, "wavelength": 0.099, "sample_detector_distance": 2.867, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.054, "s_max": 4.846, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDED5_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/SASDED5_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_fit_img.png", "software": "CRYSOL", "chi_square_value": 23.927, "p_value": 0.0, "fit_residual_plot": "BSA_monomer_4f5s00_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDED5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BSA_monomer_4f5s00.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDED5_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/SASDED5_fit2_model1.pdb", "model_mw": 50.679, "bead_radius": 2.75, "log": "https://www.sasbdb.org/media/log_files/BM29_SEC_96p_damsel.log", "symmetry": "P1", "comment": null, "user": 365 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/BM29_SEC_96p_01_fit_img.png", "software": "DAMMIF", "chi_square_value": 65.208, "p_value": 0.0, "fit_residual_plot": "BM29_SEC_96p_01_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDED5_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BM29_SEC_96p_01.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "BayesApp", "pddf_software_version": null, "i0_calibration_standard": null, "description": "The BSA sample (500 microlitres at 8.1 mg/ml) was injected onto a GE Healthcare S200 Increase 10/300 (24 ml) column at a flow rate of 0.7 ml/min at 10°C. A total of 1850 x 1 second SAXS data frames were recorded throughout the BSA elution. After background solvent corrections, SEC-SAXS data frames 1221 - 1260, corresponding to monomeric BSA, were scaled, averaged and binned logarithmically to produce the data displayed in this entry. Additional files, including plots the selected frames and of I(0), HPLC UV trace and Rg vs. time (determined by AUTORG) are included in the additional files of the full entry zip archive.", "experiment_description": "Synchrotron SAXS data from solutions of Bovine serum albumin monomer using SEC-SAXS in PBS plus 1 mM DTT, pH 7.4 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle).", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 63.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 63.0, "porod_mw_error": null, "pddf_i0": 61.73576, "pddf_i0_error": null, "guinier_i0": 4.886, "guinier_i0_error": 0.00183, "pddf_rg": 2.71, "pddf_rg_error": null, "guinier_rg": 2.695, "guinier_rg_error": 0.002, "pddf_dmax": 8.71, "pddf_dmax_error": null, "porod_volume": 84.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 43, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDED5_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }