{ "code": "SASDF65", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.", "publication": { "title": "Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.", "author_list": "Srivastava D, Gakhar L, Artemyev NO", "journal": "Nat Commun", "doi": "10.1038/s41467-019-11088-x", "pmid": "31300652", "published_date": "2019 Jul 12" }, "status": "released", "submitted_date": "2019-03-27", "released_date": "2019-06-17" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF65.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF65.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF65_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF65_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF65.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 X 1M", "resolution": 0.172 }, "name": "Advanced Photon Source (APS), Argonne National Laboratory", "city": "Lemont, IL", "country": "USA", "beamline_name": "BioCAT 18ID", "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": "Resistance to inhibitors of cholinesterase 8 homolog A", "short_name": "Ric8a", "sequence": "GHMADPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\r\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\r\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\r\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\r\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\r\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\r\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\r\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\r\nKLVNMFDKLSRH", "organism": "Bos taurus", "uniprot_code": "Q5E9J8", "uniprot_range_first": 1, "uniprot_range_last": 492, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MEPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\nKLVNMFDKLSRHRVIQPMGMSPRGQLTSLQDAMCETMEGQLSSDPDSDPD", "mw": 55.643, "total_mw": 55.643, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Resistance to inhibitors of cholinesterase 8 homolog A (Ric8a) amino acids 1-492", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Iowa, USA", "full_name": "University of Iowa", "webpage": "https://uiowa.edu/" } ], "contributor_name": "Dhiraj", "contributor_surname": "Srivastava", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-10-27", "storage_temperature": 4.0, "cell_temperature": 25.0, "exposure_time": 0.5, "number_of_frames": null, "wavelength": 0.1033, "sample_detector_distance": 3.5, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.054, "s_max": 3.813, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit1_model1_img.png", "software": "BILBOMD", "pdb_link": [ { "pdb_code": "6n85", "ext_code": "6N85", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit1_model1.pdb", "model_mw": 55.35, "bead_radius": null, "log": null, "symmetry": null, "comment": "One state model", "user": 431 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF65_single_state_model_corrected_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 1.507476, "p_value": 0.000294, "fit_residual_plot": "SASDF65_single_state_model_corrected_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF65_fit1.dat", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model1_img.png", "software": "BILBOMD", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model1.pdb", "model_mw": 137.9, "bead_radius": null, "log": null, "symmetry": null, "comment": "Fractional contribution in X-ray scattering: 59%", "user": 431 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model2_img.png", "software": "BILBOMD", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model2.pdb", "model_mw": 137.9, "bead_radius": null, "log": null, "symmetry": null, "comment": "Fractional contribution in X-ray scattering: 29%", "user": 431 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF65_fit2_model3_img.png", "software": "BILBOMD", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF65_fit2_model3.pdb", "model_mw": 137.9, "bead_radius": null, "log": null, "symmetry": null, "comment": "Fractional contribution in X-ray scattering: 12%", "user": 431 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF65_multi_state_model_corrected_fitfoxs_img.png", "software": "MES-FoXS", "chi_square_value": 1.198522, "p_value": 0.004708, "fit_residual_plot": "SASDF65_multi_state_model_corrected_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF65_fit2.dat", "fit_log": null, "software_version": null, "description": "Three state model, the fractional contributions in X-ray scattering from the first, second and third states are 0.59, 0.29 and 0.12 respectively." } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Ric8a 1-492 in 20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 25°C. 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": 64.6, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 55.0, "porod_mw_error": null, "pddf_i0": 0.002138, "pddf_i0_error": null, "guinier_i0": 0.00212099, "guinier_i0_error": 2e-06, "pddf_rg": 3.5, "pddf_rg_error": null, "guinier_rg": 3.37, "guinier_rg_error": 0.1, "pddf_dmax": 12.7, "pddf_dmax_error": null, "porod_volume": 88.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 25, "guinier_point_last": 111, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF65_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }