{ "code": "SASDVZ5", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52", "publication": { "title": "A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52", "author_list": "Struble L, Lovelace J, Borgstahl G", "journal": "Journal of Structural Biology", "doi": "10.1016/j.jsb.2024.108115", "pmid": null, "published_date": "2024 Sep" }, "status": "released", "submitted_date": "2024-08-07", "released_date": "2024-08-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVZ5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVZ5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVZ5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVZ5.sascif", "experiment": { "instrument": { "detector": { "type": "Photon Counter", "name": "Pilatus 100K-S", "resolution": 172.0 }, "name": "Eppley Structural Biology Facility, University of Nebraska Medical Center", "city": "Omaha, NE", "country": "United States of America", "beamline_name": "Rigaku BioSAXS 1000", "beam_geometry": null, "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": "DNA repair protein RAD52 homolog", "short_name": "RAD52", "sequence": "MSGTEEAILGGRDSHPAAGGGSVLCFGQCQYTAEEYQAIQKALRQRLGPEYISSRMAGGGQKVCYIEGHRVINLANEMFGYNGWAHSITQQNVDFVDLNNGKFYVGVCAFVRVQLKDGSYHEDVGYGVSEGLKSKALSLEKARKEAVTDGLKRALRSFGNALGNCILDKDYLRSLNKLPRQLPLEVDLTKAKRQDLEPSVEEARYNSCRPNM", "organism": "Homo sapiens", "uniprot_code": "P43351", "uniprot_range_first": 1, "uniprot_range_last": 212, "oligomerization": "decamer", "molecular_type": "protein", "uniprot_sequence": "MSGTEEAILGGRDSHPAAGGGSVLCFGQCQYTAEEYQAIQKALRQRLGPEYISSRMAGGG\nQKVCYIEGHRVINLANEMFGYNGWAHSITQQNVDFVDLNNGKFYVGVCAFVRVQLKDGSY\nHEDVGYGVSEGLKSKALSLEKARKEAVTDGLKRALRSFGNALGNCILDKDYLRSLNKLPR\nQLPLEVDLTKAKRQDLEPSVEEARYNSCRPNMALGHPQLQQVTSPSRPSHAVIPADQDCS\nSRSLSSSAVESEATHQRKLRQKQLQQQFRERMEKQQVRVSTPSAEKSEAAPPAPPVTHST\nPVTVSEPLLEKDFLAGVTQELIKTLEDNSEKWAVTPDAGDGVVKPSSRADPAQTSDTLAL\nNNQMVTQNRTPHSVCHQKPQAKSGSWDLQTYSADQRTTGNWESHRKSQDMKKRKYDPS", "mw": 23.4, "total_mw": 234.0, "number_molecules": 10, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The crystallisable N-terminal half of the hRAD52 protein." } ], "buffer": { "name": "20 mM Bis-Tris, 10% glycerol, 400 mM NaCl, 100 mM KCl, 1 mM EDTA", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.0, "deuteration": null }, "purity_method": null, "name": "Human DNA repair protein RAD52 homolog (amino acids 1-212)", "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": "University of Nebraska Medical Center", "webpage": null } ], "contributor_name": "Lucas", "contributor_surname": "Struble", "orcid": "https://orcid.org/0000-0002-0671-259X" } ], "concentration_method": null, "concentration_unit": null, "date": "2014-07-25", "storage_temperature": 15.0, "cell_temperature": 15.0, "exposure_time": 9000.0, "number_of_frames": 1, "wavelength": 0.154, "sample_detector_distance": 0.48, "concentration_min": null, "concentration_max": 7.48, "sample_volume": null, "flow_rate": null, "s_min": 0.066, "s_max": 6.854, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVZ5_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "dammif (r3203)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVZ5_fit1_model1.pdb", "model_mw": 227.5, "bead_radius": 2.5, "log": "https://www.sasbdb.org/media/log_files/1_7.48mg_1-7_uYHNtVa.log", "symmetry": null, "comment": null, "user": 1034 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVZ5_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 2.157961, "p_value": 0.0, "fit_residual_plot": "SASDVZ5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVZ5_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/1_7.48mg_1-7_9uFrvmW.log", "software_version": "dammif (r3203)", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.5a", "i0_calibration_standard": null, "description": "Using SEC-MALS the molecular weight is closest to that expected for a 10-mer. The data used to calculate the P(r) profile, and subsequent DAM modelling has been normalized to protein concentration in mg/mL.", "experiment_description": "SAXS data from solutions of the human DNA repair protein RAD52 homolog (amino acids 1-212) in 20 mM Bis-Tris, 10% glycerol, 400 mM NaCl, 100 mM KCl, 1 mM EDTA, pH 6 were collected using a Rigaku/ BioSAXS1000 instrument at the Eppley Structural Biology Facility (University of Nebraska Medical Center, Omaha, NE, USA) equipped with a Dectris/Pilatus 100K-S detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 7.48 mg/ml was measured at 15°C. One 9000 second frame was 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": 229.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 227.1, "porod_mw_error": null, "pddf_i0": 1.064, "pddf_i0_error": null, "guinier_i0": 8.03743, "guinier_i0_error": null, "pddf_rg": 3.96, "pddf_rg_error": null, "guinier_rg": 4.058, "guinier_rg_error": 0.161, "pddf_dmax": 11.77, "pddf_dmax_error": null, "porod_volume": 375.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 4, "guinier_point_last": 18, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVZ5_datloglog_img.png", "symmetry": null, "last_modified": "2024-09-11T17:07:38.499123+02:00", "bragg_peak": [] }