{"code":"SASDXH7","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Probing the statistics of sequence-dependent DNA conformations in solution using SAXS.","publication":{"title":"Probing the statistics of sequence-dependent DNA conformations in solution using SAXS.","author_list":"Koning HJ, Pullakhandam A, Whitten AE, Bond CS, Peyrard M","journal":"Acta Crystallogr D Struct Biol","doi":"10.1107/S2059798325011556","pmid":"41553140","published_date":"2026 Feb 1"},"status":"released","submitted_date":"2024-09-18","released_date":"2025-08-12"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDXH7.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDXH7.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXH7_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXH7_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXH7_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXH7_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDXH7.sascif","experiment":{"instrument":{"detector":{"type":"Dectris","name":"Pilatus 1M","resolution":172.0},"name":"Australian  Synchrotron","city":"Melbourne","country":"Australia","beamline_name":"SAXS/WAXS","beam_geometry":"Point","type_of_source":"X-ray synchrotron","point_source":true,"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":"GAGE6 60bp dsDNA oligo","short_name":"GAGE6 oligo","sequence":"GCCTTCTGCAAAGAAGTCTTGCGCATCTTTTGTGAAGTTTATTTCTAGCTTTTTGATGCT","organism":"Homo sapiens","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"DNA","uniprot_sequence":"","mw":37.101,"total_mw":37.101,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"60 bp GAGE6 dsDNA oligonucleotide from the study 'insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1' (Wang et al, 2022)."}],"buffer":{"name":"150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTT","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"GAGE6 60bp dsDNA oligonucleotide","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":null,"full_name":"The University of Western Australia","webpage":null}],"contributor_name":"Heidar","contributor_surname":"Koning","orcid":""}],"concentration_method":null,"concentration_unit":null,"date":"2023-03-14","storage_temperature":null,"cell_temperature":null,"exposure_time":null,"number_of_frames":null,"wavelength":null,"sample_detector_distance":null,"concentration_min":null,"concentration_max":null,"sample_volume":null,"flow_rate":null,"s_min":0.045,"s_max":4.921,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDXH7_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"ATSAS online","model_data":"https://www.sasbdb.org/media/pdb_file/SASDXH7_fit1_model1.pdb","model_mw":null,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/GAGE6_2.log","symmetry":"P1","comment":"DAMMAVER search area used in DAMMIN","user":726}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXH7_fit1_fixed_fit_img.png","software":"DAMMIN","chi_square_value":0.357,"p_value":0.6005,"fit_residual_plot":"SASDXH7_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDXH7_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/GAGE6_2.log","software_version":"ATSAS online","description":"DAMMAVER search envelope which had some curvature used as a search model in DAMMIN"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Data was collected at the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus3 S 2M detector at a sample-detector distance of 2.68 m and at a wavelength of λ = 0.107812 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50 μl sample at 2.587 mg/ml was injected onto a GE Superdex 200 5/150 column at 25°C using 150 mM KCl, 20 mM HEPES (pH 7.4), 5 mM MgCl2, 1 mM DTT, 5% glycerol buffer. 400 successive 1 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. 2sigma errors from the Australian Synchrotron's SAXS/WAXS beamline have been divided by 2 to be compatible with expectations from the ATSAS package\r\n\r\nThis is the 60 bp GAGE6 oligo from Lee et al (2015); Wang et al (2022) which reportedly binds SFPQ. SAXS analysis indicates some degree of curvature which is likely due to the presence of multiple AT repeat regions in the sequence.","experiment_description":null,"tags":[],"intensity_unit":"arbitrary","experimental_mw":33.1,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":63.0,"porod_mw_error":null,"pddf_i0":0.005087,"pddf_i0_error":null,"guinier_i0":0.00486542,"guinier_i0_error":null,"pddf_rg":5.52,"pddf_rg_error":null,"guinier_rg":4.785,"guinier_rg_error":2.34,"pddf_dmax":19.5,"pddf_dmax_error":null,"porod_volume":101.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":3,"guinier_point_last":33,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDXH7_datloglog_img.png","symmetry":null,"last_modified":"2026-02-23T09:45:35.560463+01:00","bragg_peak":[]}