{ "code": "SASDVS5", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation.", "publication": { "title": "Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation.", "author_list": "Lin TC, Shih O, Tsai TY, Yeh YQ, Liao KF, Mansel BW, Shiu YJ, Chang CF, Su AC, Chen YR, Jeng US", "journal": "IUCrJ", "doi": "10.1107/S2052252524006341", "pmid": "39120045", "published_date": "2024 Sep 1" }, "status": "released", "submitted_date": "2024-08-01", "released_date": "2024-08-07" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVS5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVS5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVS5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVS5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVS5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVS5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVS5.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger X 1M & 9M", "resolution": 0.001 }, "name": "NSRRC", "city": "Hsinchu", "country": "Taiwan", "beamline_name": "TPS13A", "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": "Isoform Short of Small EDRK-rich factor 1", "short_name": null, "sequence": "MARGNQRELARQKNMKKTQEISKGKRKEDSLTASQRKQRDSEIMQEKQKAANEKKSMQTREK", "organism": "Homo sapiens", "uniprot_code": "O75920", "uniprot_range_first": 1, "uniprot_range_last": 62, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MARGNQRELARQKNMKKTQEISKGKRKEDSLTASQRKQRDSEIMQEKQKAANEKKSMQTR\nEK", "mw": 7.336, "total_mw": 7.336, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "HTT3", "short_name": null, "sequence": "MATPEKPMKAFESPKSFPQQPQQQPQQPQQQYK", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 3.887, "total_mw": 3.887, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "Sodium phosphate buffer", "concentration_unit": null, "comment": "(PB) solution (containing 480 μL of 10 mM PB, pH 7.4, 16.5 μL of 100 mM NaOH, and 10 μL of 1% TFA)", "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Small EDRK-rich factor 1 (SERF1a) bound to HTT-3 peptide", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Hsinchu City, Taiwan", "full_name": "National Synchrotron Radiation Research Center", "webpage": "https://www.nsrrc.org.tw/" } ], "contributor_name": "Orion", "contributor_surname": "Shih", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2021-05-20", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 2.0, "number_of_frames": 5, "wavelength": 0.08265, "sample_detector_distance": 2.5, "concentration_min": 0.5, "concentration_max": 0.8, "sample_volume": 70.0, "flow_rate": 0.35, "s_min": 0.126, "s_max": 2.953, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVS5_fit1_model1_img.png", "software": "Rosetta", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVS5_fit1_model1.pdb", "model_mw": 11.26, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 216 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVS5_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 2.2084, "p_value": 0.2523, "fit_residual_plot": "SASDVS5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVS5_fit1.fit", "fit_log": null, "software_version": "3.2.1", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The sodium phosphate buffer solution contains 480 μL of 10 mM PB, pH 7.4, 16.5 μL of 100 mM NaOH, and 10 μL of 1% trifluoroacetic acid (TFA). CAUTION: Severe steric clashes noted in the model.", "experiment_description": "Synchrotron SAXS data from solutions of small EDRK-rich factor 1 (SERF1a) bound to HTT-3 peptide in sodium phosphate buffer, pH 7.4 were collected on the TPS13A beam line at the NSRRC (Hsinchu, Taiwan) using a Eiger X 1M & 9M detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.08265 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 0.8 mg/ml were measured at 10°C. Five successive 2 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 6.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.008304, "pddf_i0_error": null, "guinier_i0": 0.00860341, "guinier_i0_error": null, "pddf_rg": 2.21, "pddf_rg_error": null, "guinier_rg": 2.3, "guinier_rg_error": 0.341, "pddf_dmax": 7.16, "pddf_dmax_error": null, "porod_volume": 8.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 35, "guinier_point_last": 119, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVS5_datloglog_img.png", "symmetry": null, "last_modified": "2024-08-18T16:49:41.246068+02:00", "bragg_peak": [] }