{"code":"SASDDR4","status":"Published","type_of_curve":"Extrapolated to infinite dilution","angular_unit":"1/A","project":{"title":"Mutation in a flexible linker modulates binding affinity for modular complexes.","publication":{"title":"Mutation in a flexible linker modulates binding affinity for modular complexes.","author_list":"Stokes PH, Robertson NO, Silva AP, Estephan T, Trewhella J, Guss JM, Matthews JM","journal":"Proteins","doi":"10.1002/prot.25675","pmid":"30788856","published_date":"2019 Feb 20"},"status":"released","submitted_date":"2017-09-27","released_date":"2019-03-01"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDDR4.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDDR4.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR4_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR4_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDR4_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR4_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDDR4.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":"LIM/homeobox protein Lhx4","short_name":"Lhx4-LIM domains","sequence":"GSMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQ","organism":"Mus musculus","uniprot_code":"P53776","uniprot_range_first":24,"uniprot_range_last":149,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MMQSAAVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADC\nQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIIC\nNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSP\nKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGGSKQ\nEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQ\nDLRDGSPYGIPQSPSSISSLPSHAPLLNGLDYTVDSNLGIIAHAGQGVSQTLRAMAGGPT\nSDLSTGSSVGYPDFPTSPASWLDEMDHPPF","mw":14.712,"total_mw":14.712,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Insulin gene enhancer protein ISL-2 (R282G)","short_name":"ISL-2 (R282G)","sequence":"GGSGGHMGSGGGTPLVAGSPIGHENAVQGSAVEVQTYQPPW","organism":"Mus musculus","uniprot_code":"Q9CXV0","uniprot_range_first":273,"uniprot_range_last":301,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MVDIIFHYPFLGAMGDHSKKKPGTAMCVGCGSQIHDQFILRVSPDLEWHAACLKCAECSQ\nYLDETCTCFVRDGKTYCKRDYVRLFGIKCAQCQVGFSSSDLVMRARDSVYHIECFRCSVC\nSRQLLPGDEFSLREHELLCRADHGLLLERAAAGSPRSPGPLPGARGLHLPDAGSGRQPSL\nRTHVHKQAEKTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQ\nNKRCKDKKKSILMKQLQQQQHSDKASLQGLTGTPLVAGSPIRHENAVQGSAVEVQTYQPP\nWKALSEFALQSDLDQPAFQQLVSFSESGSLGNSSGSDVTSLSSQLPDTPNSMVPSPVET","mw":3.932,"total_mw":3.932,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM Tris, 150 mM NaCl, 1 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"LIM/homeobox protein Lhx4 LIM domains fused to the LIM interaction domain (LID) R282G mutant of Insulin gene enhancer protein ISL-2","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Sydney, Australia","full_name":"School of Life and Environmental Science, University of Sydney","webpage":"http://sydney.edu.au/science/life-environment/"}],"contributor_name":"Philippa","contributor_surname":"Stokes","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2015-11-19","storage_temperature":null,"cell_temperature":13.5,"exposure_time":1.0,"number_of_frames":24,"wavelength":0.10332,"sample_detector_distance":null,"concentration_min":0.2,"concentration_max":1.9,"sample_volume":null,"flow_rate":null,"s_min":0.064,"s_max":3.277,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDDR4_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDDR4_fit1_model1.pdb","model_mw":13.802,"bead_radius":2.2,"log":null,"symmetry":null,"comment":"One of 20 models generated using DAMMIN that went into creating the Damfilt model.","user":205},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDDR4_fit1_model2_img.png","software":"DAMFILT","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDDR4_fit1_model2.pdb","model_mw":13.721,"bead_radius":2.0,"log":"https://www.sasbdb.org/media/log_files/damsup_Dn1jpbJ.log","symmetry":null,"comment":"Damfilt model derived from multiple DAMMIN runs where 20 models were generated, spatially aligned.","user":205}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/DM7GExtr_fit_img.png","software":"DAMMIN","chi_square_value":4.442,"p_value":0.549514,"fit_residual_plot":"DM7GExtr_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDDR4_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/DM7GExtr.log","software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The protein anaysed is a fusion of two interacting partners: the LIM domains of Lhx4 and the LID of Isl2, with a point mutation within the Isl2-LID (R282G). The ab initio bead models presented in this entry include: 1) The best-fit individual reconstruction (top) and; 2) The spatially aligned and volume/bead occupancy-corrected averaged representation of the protein in solution (bottom) calculated from twenty individual reconstructions (NSD = 0.67; resolution estimate = 2.8 nm). Five concentrations of protein were subjected to SAXS as static samples (96-well plate) at the Australian Synchrotron. Subtle concentration dependent effects were noted. All data and additional information relating to the concentration series is included in the full-entry zip archive. The protein was subjected to SEC (off line) as the last purification step just prior to data collection. Also refer to the related SASBDB entry SASDDQ4.","experiment_description":"Synchrotron SAXS data from solutions of the LIM domains of LIM/homeobox protein Lhx4 fused to the LIM interaction domain (LID; R282G mutant) of the insulin gene enhancer protein ISL-2 in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.2 and 1.9 mg/ml were measured at 13.5°C. 24 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. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.","tags":[],"intensity_unit":"arbitrary","experimental_mw":15.0,"experimental_mw_error":null,"guinier_i0_mw":17.0,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":0.03409,"pddf_i0_error":5e-05,"guinier_i0":0.03394,"guinier_i0_error":4e-05,"pddf_rg":2.36,"pddf_rg_error":0.005,"guinier_rg":2.27,"guinier_rg_error":0.01,"pddf_dmax":8.47,"pddf_dmax_error":null,"porod_volume":20.7,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":10,"guinier_point_last":131,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDDR4_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}