{ "code": "SASDE38", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain", "publication": { "title": "Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain", "author_list": "Salzano G, Brennich M, Mancini G, Tran T, Legname G, D’Angelo P, Giachin G", "journal": "Biophysical Journal", "doi": "10.1016/j.bpj.2019.12.025", "pmid": null, "published_date": "2020 Jan" }, "status": "released", "submitted_date": "2018-11-13", "released_date": "2019-11-25" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDE38.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDE38.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE38_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE38_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDE38_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE38_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDE38.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": "Major prion protein", "short_name": null, "sequence": "GQGGSHSQWNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSVMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVQTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS", "organism": "Ovis aries", "uniprot_code": "P23907", "uniprot_range_first": 94, "uniprot_range_last": 234, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MVKSHIGSWILVLFVAMWSDVGLCKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGW\nGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGSHSQWNKPSKPKTNMKHVAGAAA\nAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYSNQNNFVH\nDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGASVILFSS\nPPVILLISFLIFLIVG", "mw": 16.085, "total_mw": 16.085, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM Ammonium Acetate, 250 mM NaCl, 0.001 mM CuSO4", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 5.5, "deuteration": null }, "purity_method": null, "name": "C-terminal truncated ovine prion protein (94-234) with VRQ polymorphism + Cu(II)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "ESRF", "address": "Grenoble, France", "full_name": "European Synchrotron Radiation Facility", "webpage": "http://www.esrf.eu/" } ], "contributor_name": "Gabriele", "contributor_surname": "Giachin", "orcid": "https://orcid.org/0000-0001-7550-0307" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-05-04", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 1, "wavelength": 0.099, "sample_detector_distance": 2.864, "concentration_min": null, "concentration_max": 7.0, "sample_volume": null, "flow_rate": null, "s_min": 0.103, "s_max": 4.928, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE38_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDE38_fit1_model1.pdb", "model_mw": 16.02, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/logFile_001_1_YmXnJKW.log", "symmetry": "P1", "comment": null, "user": 388 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDE38_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 3.578, "p_value": 0.864685, "fit_residual_plot": "SASDE38_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE38_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_8RO0wJ6.log", "software_version": null, "description": "" } ], "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 the C-terminal truncated ovine prion protein (94-234) with VRQ polymorphism in 25 mM ammonium acetate, 250 mM NaCl, 0.001 mM CuSO4, pH 5.5 were collected using size exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a 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). SEC-SAXS was performed at 20 °C using the following parameters: Column type, Superdex 200 5/150 GL (GE Healthcare); Flow rate: 0.15 mL/min; Total acquisition time: 25 min; Injection concentration: 7 mg/mL; Injection volume: 50 μL. The data obtained through the sample elution peak (865-905 1 s frames) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 16.1, "experimental_mw_error": null, "guinier_i0_mw": 15.5, "guinier_i0_mw_error": null, "porod_mw": 15.6, "porod_mw_error": null, "pddf_i0": 11.52, "pddf_i0_error": null, "guinier_i0": 10.93, "guinier_i0_error": 0.03, "pddf_rg": 2.417, "pddf_rg_error": null, "guinier_rg": 2.15, "guinier_rg_error": 0.01, "pddf_dmax": 8.7, "pddf_dmax_error": null, "porod_volume": 28.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 57, "guinier_point_last": 113, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDE38_datloglog_img.png", "symmetry": null, "last_modified": "2020-08-28T15:28:10.454623+02:00", "bragg_peak": [] }