{"code":"SASDVV4","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"A conserved viral RNA fold enables nuclease resistance across kingdoms of life.","publication":{"title":"A conserved viral RNA fold enables nuclease resistance across kingdoms of life.","author_list":"Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL","journal":"Nucleic Acids Res","doi":"10.1093/nar/gkaf840","pmid":"40884403","published_date":"2025 Aug 27"},"status":"released","submitted_date":"2024-07-12","released_date":"2025-07-12"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVV4.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVV4.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV4_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV4_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVV4_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV4_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVV4.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 S 1M","resolution":172.0},"name":"National Synchrotron Light Source II (NSLS-II)","city":"Upton, NY","country":"USA","beamline_name":"16-ID (LiX)","beam_geometry":null,"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":"ST9 WT (54 nt RNA)","short_name":null,"sequence":"AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGUAGGCA","organism":null,"uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"RNA","uniprot_sequence":"","mw":17.484,"total_mw":17.484,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3","concentration_unit":null,"comment":"10 mM MgCl2 buffer","additive":null,"concentration":null,"pka":null,"ph":null,"deuteration":null},"purity_method":null,"name":"ST9a RNA, WT (54 nucleotides in 10 mM MgCl2; monomer)","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":"Columbia University Irving Medical Center","webpage":null}],"contributor_name":"Sophie","contributor_surname":"Korn","orcid":"https://orcid.org/0000-0003-3798-3277"}],"concentration_method":null,"concentration_unit":null,"date":"2024-03-23","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":2.0,"number_of_frames":1500,"wavelength":0.082,"sample_detector_distance":4.065,"concentration_min":null,"concentration_max":3.0,"sample_volume":95.0,"flow_rate":0.75,"s_min":0.06,"s_max":31.9,"total_exposure_time":null,"seccolumn":1},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVV4_fit1_model1_img.png","software":"PyMOL","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVV4_fit1_model1.pdb","model_mw":17.12,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1092}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVV4_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":0.876,"p_value":0.0,"fit_residual_plot":"SASDVV4_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVV4_fit1.fit","fit_log":null,"software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":null,"i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of ST9 RNA WT, (54 nucleotides) in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II; Upton, NY, USA) using a Pilatus3 S 1M detector at a sample-detector distance of 4.1 m and at a wavelength of λ = 0.082 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 95.00 μl sample at 3 mg/ml was injected at a 0.75 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 1500 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.","tags":[],"intensity_unit":"arbitrary","experimental_mw":13.5,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":2.858,"pddf_i0_error":null,"guinier_i0":2.90113,"guinier_i0_error":null,"pddf_rg":1.795,"pddf_rg_error":null,"guinier_rg":1.85,"guinier_rg_error":0.011,"pddf_dmax":5.83,"pddf_dmax_error":null,"porod_volume":20.8,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":9,"guinier_point_last":47,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVV4_datloglog_img.png","symmetry":null,"last_modified":"2025-09-01T15:31:28.502669+02:00","bragg_peak":[]}