{"code":"SASDGD5","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand","publication":{"title":"The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand","author_list":"Rodzli N, Lockhart-Cairns M, Levy C, Chipperfield J, Bird L, Baldock C, Prince S","journal":"Biophysical Journal","doi":"10.1016/j.bpj.2020.06.018","pmid":null,"published_date":"2020 Jun"},"status":"released","submitted_date":"2019-09-16","released_date":"2019-09-20"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDGD5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDGD5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGD5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGD5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGD5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGD5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDGD5.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"Diamond Light Source","city":"Didcot","country":"UK","beamline_name":"B21","beam_geometry":"1 x 5 mm","type_of_source":"X-ray 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mM TRIS/HCl, 150 mM NaCl + 10 mM RRESEI","concentration_unit":null,"comment":"standard buffer plus 10mM ligand peptide","additive":null,"concentration":null,"pka":null,"ph":8.5,"deuteration":null},"purity_method":null,"name":"The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (Paused SEC)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Manchester, UK","full_name":"University of Manchester","webpage":"http://www.manchester.ac.uk/"}],"contributor_name":"Stephen","contributor_surname":"Prince","orcid":"https://orcid.org/0000-0003-0929-0254"}],"concentration_method":null,"concentration_unit":null,"date":"2016-01-26","storage_temperature":null,"cell_temperature":null,"exposure_time":10.0,"number_of_frames":69,"wavelength":0.1,"sample_detector_distance":3.9,"concentration_min":null,"concentration_max":15.0,"sample_volume":20.0,"flow_rate":0.0,"s_min":0.171,"s_max":3.997,"total_exposure_time":null,"seccolumn":19},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model1_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model1.pdb","model_mw":21.7,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model2_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model2.pdb","model_mw":21.12,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model3_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model3.pdb","model_mw":21.12,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model4_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model4.pdb","model_mw":43.02,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model5_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model5.pdb","model_mw":86.04,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model6_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model6.pdb","model_mw":172.1,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model7_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model7.pdb","model_mw":258.1,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model8_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model8.pdb","model_mw":344.2,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model9_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model9.pdb","model_mw":430.2,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGD5_fit1_model10_img.png","software":"Other","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGD5_fit1_model10.pdb","model_mw":516.2,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SEC-LIG-Jan16-clo_fixed_fit_img.png","software":"OLIGOMER","chi_square_value":3.71,"p_value":0.0,"fit_residual_plot":"SEC-LIG-Jan16-clo_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDGD5_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/oligo_SEC-LIG-Jan16-clo.log","software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Scattering data are fitted using the ATSAS OLIGOMER program using a suite of models. The ATSAS program FFMAKER was used to generate form factors for each model in the suite. Each model is assigned a volume fraction to fit the observed scattering profile. 3 monomer models are included, the first is a compact conformation of PDZ1-2 similar to PDB entries 6spv/6spz; the other two are domain models obtained from a representative run of the ATSAS EOM program with data projected to infinite dilution. Multimeric models are drawn from a \"clustering Spacegroup\", unit cell 14.8nm symmetry I2(1)3, and consist of identical copies of an extended conformation of PDZ1-2 (similar to PDB entry 3zrt) assembled by symmetry operations. \r\n\r\nIn the order of deposition:\r\nModel number; Stoichiometry; MW (kDa); source; Volume fraction. \r\n 1; 1; 21; Crystal Structure; 0.381.\r\n 2; 1; 21; EOM; 0.091.\r\n 3; 1; 21; EOM; 0.470.\r\n 4; 2; 42; clustering Spacegroup; 0.042.\r\n 5; 4; 84; clustering Spacegroup; 0.015.\r\n 6; 8; 168; clustering Spacegroup; 0.000.\r\n 7; 12, 252; clustering Spacegroup; 0.001.\r\n 8; 16, 336, clustering Spacegroup; 0.000.\r\n 9; 20, 420, clustering Spacegroup; 0.000.\r\n 10; 24, 504, clustering Spacegroup; 0.001.","experiment_description":"Synchrotron SAXS data from solutions of the PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (Paused SEC) in 20 mM TRIS/HCl, 150 mM NaCl + 10 mM RRESEI, pH 8.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and at a wavelength of λ = 0.1 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 20.00 μl sample at 15 mg/ml was injected at a 0.00 ml/min flow rate onto a Shodex KW403 column . 69 successive 10 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":20.8,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":18.0,"porod_mw_error":null,"pddf_i0":0.009483,"pddf_i0_error":null,"guinier_i0":0.0095,"guinier_i0_error":0.0001,"pddf_rg":2.34,"pddf_rg_error":null,"guinier_rg":2.334,"guinier_rg_error":0.072,"pddf_dmax":6.84,"pddf_dmax_error":null,"porod_volume":28.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":40,"guinier_point_last":140,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDGD5_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}