{"code":"SASDGE5","status":"Published","type_of_curve":"Single concentration","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/SASDGE5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDGE5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGE5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDGE5.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"PETRA III","city":"DESY; Hamburg","country":"Germany","beamline_name":"EMBL P12","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":"PDZ1-2 fragment of PSD-95/Disks large homolog 4","short_name":"PDZ1-2","sequence":"GPGTEGEMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRV\r\nNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFS\r\nIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALK\r\nNTYDVVYLKVAKPSNA","organism":"Homo sapiens","uniprot_code":"P78352","uniprot_range_first":55,"uniprot_range_last":249,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MDCLCIVTTKKYRYQDEDTPPLEHSPAHLPNQANSPPVIVNTDTLEAPGYELQVNGTEGE\nMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFV\nNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVGN\nQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVY\nLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYSPVAKD\nLLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQIL\nSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGT\nASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDS\nETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQMEVHYARPIIIL\nGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIE\nAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLE\nINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPA\nRERL","mw":20.8,"total_mw":20.8,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM TRIS/HCl, 150 mM NaCl","concentration_unit":null,"comment":null,"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)","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":"2015-06-11","storage_temperature":15.0,"cell_temperature":15.0,"exposure_time":0.05,"number_of_frames":13,"wavelength":0.123987,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":15.0,"sample_volume":null,"flow_rate":null,"s_min":0.085,"s_max":4.799,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGE5_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/SASDGE5_fit1_model1.pdb","model_mw":20.12,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGE5_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/SASDGE5_fit1_model2.pdb","model_mw":19.54,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGE5_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/SASDGE5_fit1_model3.pdb","model_mw":19.54,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGE5_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/SASDGE5_fit1_model4.pdb","model_mw":39.87,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":486},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGE5_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/SASDGE5_fit1_model5.pdb","model_mw":79.74,"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/CON-APO-Jun15-clo_fixed_fit_img.png","software":"OLIGOMER","chi_square_value":6.31,"p_value":0.0,"fit_residual_plot":"CON-APO-Jun15-clo_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDGE5_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/oligo_CON-APO-Jun15-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\n Model number; Stoichiometry; MW (kDa); source; Volume fraction. \r\n 1; 1; 21; Crystal Structure; 0.691.\r\n 2; 1; 21; EOM; 0.237.\r\n 3; 1; 21; EOM; 0.000.\r\n 4; 2; 42; clustering Spacegroup; 0.043.\r\n 5; 4; 84; clustering Spacegroup; 0.030.","experiment_description":"Synchrotron SAXS data from solutions of the PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) in 20 mM TRIS/HCl, 150 mM NaCl, pH 8.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123987 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 15.00 mg/ml was measured at 15°C. 13 successive 0.050 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":20.0,"porod_mw_error":null,"pddf_i0":19630.0,"pddf_i0_error":null,"guinier_i0":19485.0,"guinier_i0_error":17.78,"pddf_rg":2.46,"pddf_rg_error":null,"guinier_rg":2.374,"guinier_rg_error":0.005,"pddf_dmax":9.23,"pddf_dmax_error":null,"porod_volume":32.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":4,"guinier_point_last":173,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDGE5_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}