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{
"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": []
}
