{"code":"SASDB48","status":"Published","type_of_curve":"Other","angular_unit":"1/A","project":{"title":"The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.","publication":{"title":"The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.","author_list":"Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP","journal":"Nucleic Acids Res","doi":"10.1093/nar/gkx419","pmid":"28505309","published_date":"2017 Jul 27"},"status":"released","submitted_date":"2016-11-28","released_date":"2017-05-30"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDB48.dat","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDB48.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB48_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDB48.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 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":"Major viral transcription factor ICP4","short_name":"ICP4N","sequence":"PAASAGRIERRRARAAVAGRDATGRFTAGQPRRVELDADATSG\r\nAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAA\r\nVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSF\r\nITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLAR\r\nENAALTG","organism":"Human alphaherpesvirus 1","uniprot_code":"P08392","uniprot_range_first":258,"uniprot_range_last":487,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MASENKQRPGSPGPTDGPPPTPSPDRDERGALGWGAETEEGGDDPDHDPDHPHDLDDARR\nDGRAPAAGTDAGEDAGDAVSPRQLALLASMVEEAVRTIPTPDPAASPPRTPAFRADDDDG\nDEYDDAADAAGDRAPARGREREAPLRGAYPDPTDRLSPRPPAQPPRRRRHGRWRPSASST\nSSDSGSSSSSSASSSSSSSDEDEDDDGNDAADHAREARAVGRGPSSAAPAAPGRTPPPPG\nPPPLSEAAPKPRAAARTPAASAGRIERRRARAAVAGRDATGRFTAGQPRRVELDADATSG\nAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAA\nVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSF\nITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLAR\nENAALTGAAGSPGAGADDEGVAAVAAAAPGERAVPAGYGAAGILAALGRLSAAPASPAGG\nDDPDAARHADADDDAGRRAQAGRVAVECLAACRGILEALAEGFDGDLAAVPGLAGARPAS\nPPRPEGPAGPASPPPPHADAPRLRAWLRELRFVRDALVLMRLRGDLRVAGGSEAAVAAVR\nAVSLVAGALGPALPRDPRLPSSAAAAAADLLFDNQSLRPLLAAAASAPDAADALAAAAAS\nAAPREGRKRKSPGPARPPGGGGPRPPKTKKSGADAPGSDARAPLPAPAPPSTPPGPEPAP\nAQPAAPRAAAAQARPRPVAVSRRPAEGPDPLGGWRRQPPGPSHTAAPAAAALEAYCSPRA\nVAELTDHPLFPVPWRPALMFDPRALASIAARCAGPAPAAQAACGGGDDDDNPHPHGAAGG\nRLFGPLRASGPLRRMAAWMRQIPDPEDVRVVVLYSPLPGEDLAGGGASGGPPEWSAERGG\nLSCLLAALANRLCGPDTAAWAGNWTGAPDVSALGAQGVLLLSTRDLAFAGAVEFLGLLAS\nAGDRRLIVVNTVRACDWPADGPAVSRQHAYLACELLPAVQCAVRWPAARDLRRTVLASGR\nVFGPGVFARVEAAHARLYPDAPPLRLCRGGNVRYRVRTRFGPDTPVPMSPREYRRAVLPA\nLDGRAAASGTTDAMAPGAPDFCEEEAHSHAACARWGLGAPLRPVYVALGREAVRAGPARW\nRGPRRDFCARALLEPDDDAPPLVLRGDDDGPGALPPAPPGIRWASATGRSGTVLAAAGAV\nEVLGAEAGLATPPRREVVDWEGAWDEDDGGAFEGDGVL","mw":24.31,"total_mw":48.62,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Immediate Early 3","short_name":"IE3","sequence":"CCGATCGTCCACACGGAGC","organism":null,"uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"dimer","molecular_type":"DNA","uniprot_sequence":null,"mw":5.839,"total_mw":11.678,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM HEPES, 150 mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Major viral transcription factor ICP4/Immediate Early 3 DNA (ICP4N IE3_19mer) complex","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":"Michael","contributor_surname":"Lockhart","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2015-07-27","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":null,"wavelength":0.1,"sample_detector_distance":3.9,"concentration_min":null,"concentration_max":null,"sample_volume":null,"flow_rate":null,"s_min":0.367,"s_max":2.513,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/ICP4N_refine_407_edit_cdgh_W0AmBsY_img.png","software":"PHENIX","pdb_link":[{"pdb_code":"5mhk","ext_code":"5MHK","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB48_fit1_model1.pdb","model_mw":53.44,"bead_radius":1.9,"log":null,"symmetry":"P1","comment":"","user":23}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB48_fit1_fitfoxs_img.png","software":"FoXS","chi_square_value":2.4,"p_value":0.0,"fit_residual_plot":"SASDB48_fit1_fitfoxsresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB48_fit1.dat","fit_log":null,"software_version":null,"description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDB48_fit2_model1_img.png","software":"DAMFILT","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"5.0","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB48_fit2_model1.pdb","model_mw":null,"bead_radius":2.5,"log":"https://www.sasbdb.org/media/log_files/run_1_pjjFw0m.log","symmetry":"","comment":"17 models were run in slow mode","user":23}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB48_fit2_fit_img.png","software":"DAMMIF","chi_square_value":1.34,"p_value":0.163,"fit_residual_plot":"SASDB48_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB48_fit2.fir","fit_log":null,"software_version":"","description":null}],"estimated_volume_method":null,"pddf_software":"ScÅtter","pddf_software_version":"ScÅtter 3.0g","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of Major viral transcription factor ICP4/Immediate Early 3 DNA (ICP4N IE3_19mer) complex in 20 mM HEPES, 150 mM NaCl, pH 7.4 were collected using HPLC SEC-SAXS at the B21 beam line at the Diamond Light Source (Oxfordshire, 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 = 4π sin θ/λ and 2θ is the scattering angle). The sample was separated using a Shodex KW-403 SEC column and Agilent HPLC before exposure to X-rays to isolate the ICP4N IE3_19mer complex from any dissociated monomer. 50 µL of ICP4N•IE3_19mer complex was loaded onto the Shodex column and the eluent was flowed through the SAXS beam at 0.15 mL/min; the buffer used as the background was collected after one SEC column volume. Data were collected at 20°C at one second intervals.","tags":[],"intensity_unit":null,"experimental_mw":60.4,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":109.6,"pddf_i0_error":null,"guinier_i0":114.0,"guinier_i0_error":0.44,"pddf_rg":2.51,"pddf_rg_error":null,"guinier_rg":2.54,"guinier_rg_error":0.019,"pddf_dmax":8.3,"pddf_dmax_error":null,"porod_volume":89.71,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":32,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDB48_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}