{"code":"SASDB79","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it.","publication":{"title":"Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it.","author_list":"Necasová I, Janoušková E, Klumpler T, Hofr C","journal":"Nucleic Acids Res","doi":"10.1093/nar/gkx812","pmid":"28981702","published_date":"2017 Dec 1"},"status":"released","submitted_date":"2017-01-06","released_date":"2017-09-18"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDB79.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDB79.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB79_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB79_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB79_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB79_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDB79.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 100K","resolution":172.0},"name":"CEITEC","city":"Brno","country":"Czech Republic","beamline_name":"Rigaku BioSAXS-1000","beam_geometry":"","type_of_source":"X-ray in house","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":"Basic domain of telomeric repeat-binding factor 2","short_name":"TRF2","sequence":"GPPGSMAGGGGSSDGSGRAAGRRASRSSGRARRGRHEPGLGGPAERGAG","organism":"Homo sapiens","uniprot_code":"Q15554","uniprot_range_first":42,"uniprot_range_last":86,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MAAGAGTAGPASGPGVVRDPAASQPRKRPGREGGEGARRSDTMAGGGGSSDGSGRAAGRR\nASRSSGRARRGRHEPGLGGPAERGAGEARLEEAVNRWVLKFYFHEALRAFRGSRYGDFRQ\nIRDIMQALLVRPLGKEHTVSRLLRVMQCLSRIEEGENLDCSFDMEAELTPLESAINVLEM\nIKTEFTLTEAVVESSRKLVKEAAVIICIKNKEFEKASKILKKHMSKDPTTQKLRNDLLNI\nIREKNLAHPVIQNFSYETFQQKMLRFLESHLDDAEPYLLTMAKKALKSESAASSTGKEDK\nQPAPGPVEKPPREPARQLRNPPTTIGMMTLKAAFKTLSGAQDSEAAFAKLDQKDLVLPTQ\nALPASPALKNKRPRKDENESSAPADGEGGSELQPKNKRMTISRLVLEEDSQSTEPSAGLN\nSSQEAASAPPSKPTVLNQPLPGEKNPKVPKGKWNSSNGVEEKETWVEEDELFQVQAAPDE\nDSTTNITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLG\nMN","mw":4.587,"total_mw":4.587,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"telomere DNA duplex","short_name":null,"sequence":"GTTAGGGTTAGGGTTAG\r\nCAATCCCAATCCCAATC","organism":null,"uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"DNA","uniprot_sequence":null,"mw":10.522,"total_mw":10.522,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM Tris-HCl, 50 mM LiCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":null,"full_name":"CEITEC - Central European Institute of Technology, Masaryk University","webpage":"https://www.ceitec.eu/"}],"contributor_name":"Tomas","contributor_surname":"Klumpler","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-05-03","storage_temperature":4.0,"cell_temperature":4.0,"exposure_time":3600.0,"number_of_frames":6,"wavelength":0.154,"sample_detector_distance":0.4791,"concentration_min":null,"concentration_max":2.9,"sample_volume":null,"flow_rate":null,"s_min":0.311,"s_max":3.004,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDB79_fit1_model1_img.png","software":"MONSA","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB79_fit1_model1.pdb","model_mw":null,"bead_radius":2.25,"log":"https://www.sasbdb.org/media/log_files/yCB0Wg_ABxuwwo_wY51QbU.log","symmetry":"","comment":"","user":195}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB79_fit1_fit_img.png","software":"MONSA","chi_square_value":1.061,"p_value":0.955,"fit_residual_plot":"SASDB79_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB79_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/yCB0Wg.log","software_version":"145","description":null},{"models":[],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB79_fit2_fit_img.png","software":"MONSA","chi_square_value":1.22,"p_value":0.002,"fit_residual_plot":"SASDB79_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB79_fit2.fit","fit_log":null,"software_version":"","description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"GNOM Version 5.0","i0_calibration_standard":null,"description":"The two-phase bead model of the protein-DNA complex was generated using MONSA refinement from SAXS data measured from the complex (top data-model fit) in parallel with data measured from the isolated telomeric DNA duplex (bottom data-model fit; refer to SASBDB entry SASDB89).","experiment_description":"SAXS data from solutions of the basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with a telomeric DNA duplex in 20 mM Tris-HCl, 50 mM LiCl, pH 7.5 were collected using a Rigaku BioSAXS-1000 instrument at CEITEC (Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m (I(s) vs s, where = 4πsinθ/λ; 2θ is the scattering angle and λ = 0.154 nm). Six successive 3600 second frames were collected at a sample temperature of 4°C using a solute concentration of 2.9 mg/ml. The data were normalized to the intensity of the transmitted beam and radially averaged and the corresponding scattering from the solvent-blank was subtracted to produced the scattering profile displayed in this entry.","tags":[],"intensity_unit":null,"experimental_mw":15.1,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":0.2278,"pddf_i0_error":0.001668,"guinier_i0":0.22,"guinier_i0_error":0.0018,"pddf_rg":1.776,"pddf_rg_error":0.017,"guinier_rg":1.711,"guinier_rg_error":0.058,"pddf_dmax":5.95,"pddf_dmax_error":null,"porod_volume":20.3,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":5,"guinier_point_last":32,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDB79_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}