{"code":"SASDEZ9","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations","publication":{"title":"Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations","author_list":"Solomon-Degefa H, Gebauer J, Jeffries C, Freiburg C, Meckelburg P, Bird L, Baumann U, Svergun D, Owens R, Werner J, Behrmann E, Paulsson M, Wagener R","journal":"Journal of Biological Chemistry","doi":"10.1074/jbc.RA120.014865","pmid":null,"published_date":"2020 Jul 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M","contributor_surname":"Jeffries","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2018-11-04","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":50,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":7.0,"sample_volume":null,"flow_rate":null,"s_min":0.061,"s_max":7.003,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit1_model1_img.png","software":"CORAL","pdb_link":[{"pdb_code":"4igi","ext_code":"4IGI","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"mix","software_version":"5","model_data":"https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit1_model1.pdb","model_mw":93.59,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/07N6N3.log","symmetry":"P1","comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.02,"p_value":0.553966,"fit_residual_plot":"SASDEZ9_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/07N6N300.log","software_version":"2.8.3","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit2_model1_img.png","software":"BUNCH","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":"8","model_data":"https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit2_model1.pdb","model_mw":93.57,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/N6N3Q.log","symmetry":"P1","comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit2_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.046,"p_value":0.093444,"fit_residual_plot":"SASDEZ9_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit2.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/N6N3Q00.log","software_version":"2.8.3","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit3_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit3_model1.pdb","model_mw":null,"bead_radius":1.9,"log":null,"symmetry":"P1","comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit3_fixed_fit_img.png","software":"GASBOR","chi_square_value":0.98,"p_value":0.863635,"fit_residual_plot":"SASDEZ9_fit3_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit3.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/N6B.log","software_version":"2.3i","description":""},{"models":[],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit4_fixed_fit_img.png","software":"EOM/GAJOE","chi_square_value":0.975,"p_value":0.8998,"fit_residual_plot":"SASDEZ9_fit4_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit4.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_cw2kJv9.log","software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"4.6","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of Collagen VI von Willebrand factor (VWA) four-domain fragment, N6N3 in 20 mM TRIS, 150mM NaCl 3% v/v glycerol, pH 7.4 were collected on the EMBL P12 camera at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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: GE-Healthcare S200 Increase 10/300 analytical SEC column; Flow rate: 0.6 mL/min; Sample injection concentration: 7 mg/mL; Injection volume: 75 μL. Total X-ray acquisition time = 2400 s. The data were collected through the SEC peak of the protein as a series of 50 x 1 second exposures and processed using CHROMIXS (Panjkovich & Svergun, 2018 Bioinformatics 34(11):1944-1946) that was also used to select an appropriate matched solvent-blank. Parallel inline multi-angle laser and dynamic light scattering with refractive index measurements (SEC-MALLS/DLS/RI) were performed using a Wyatt Mini-Dawn TREOS with an in-built quasi elastic light scattering (QELS) module coupled to an OptiLab T-Rex refractometer. The quoted experiential MW for this entry is derived from MALLS. Concentration-independent MW estimates obtained directly from the SAXS data using DATMW (Hajizadeh et al., 2018 Scientific Reports 8, 7204), as part of CHROMIXS/ATSAS 2.8.3, as well as the SEC-MALLS/DLS/RI data and additional modelling files, including ITASSER homology modelling (Yang et al., 2015 Nature Methods 12, 7-8) are included in the full-entry zip archive.","tags":[],"intensity_unit":"arbitrary","experimental_mw":89.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":89.0,"porod_mw_error":null,"pddf_i0":517.8,"pddf_i0_error":null,"guinier_i0":514.54,"guinier_i0_error":1.1,"pddf_rg":4.24,"pddf_rg_error":null,"guinier_rg":4.12,"guinier_rg_error":0.01,"pddf_dmax":15.6,"pddf_dmax_error":null,"porod_volume":143.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":93,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEZ9_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:55:24.740692+02:00","bragg_peak":[]}