{ "code": "SASDB89", "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/SASDB89.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB89.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB89_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB89_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB89_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB89_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB89.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": "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": "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": 60.0, "number_of_frames": 6, "wavelength": 0.154, "sample_detector_distance": 0.4791, "concentration_min": null, "concentration_max": 1.4, "sample_volume": null, "flow_rate": null, "s_min": 0.34, "s_max": 3.004, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB89_fit1_model1_img.png", "software": "MONSA", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "145", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB89_fit1_model1.pdb", "model_mw": null, "bead_radius": 2.25, "log": "https://www.sasbdb.org/media/log_files/yCB0Wg.log", "symmetry": "", "comment": "", "user": 195 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB89_fit1_fit_img.png", "software": "MONSA", "chi_square_value": 1.218, "p_value": 0.0026, "fit_residual_plot": "SASDB89_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB89_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/yCB0Wg_tooR4uK.log", "software_version": "145", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM Version 5.0", "i0_calibration_standard": null, "description": "Refer to the related SASBDB entries SASDB79 and SASDC62.", "experiment_description": "SAXS data from solutions of 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 and a solute concentration of 1.4 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": 10.5, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.09753, "pddf_i0_error": 0.001077, "guinier_i0": 0.094, "guinier_i0_error": 0.001, "pddf_rg": 1.709, "pddf_rg_error": 0.024, "guinier_rg": 1.588, "guinier_rg_error": 0.035, "pddf_dmax": 5.71, "pddf_dmax_error": null, "porod_volume": 11.9, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 34, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDB89_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }