{ "code": "SASDDG3", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with 40 bp DNA", "publication": null, "status": "released", "submitted_date": "2018-02-08", "released_date": "2019-12-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDG3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDG3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDG3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDG3.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "Sa0446 binding sequence 40bp", "short_name": "40bp dsDNA", "sequence": "GTAGTAAGATTTAAAAAAACATACTAAGATATAAATTAAC\r\nGTTAATTTATATCTTAGTATGTTTTTTTAAATCTTACTAC", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "DNA", "uniprot_sequence": null, "mw": 24.721, "total_mw": 24.721, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Transcriptional regulator Lrs14-like protein", "short_name": "AbfR2", "sequence": "MGSSHHHHHHSQDPNSMETVLQIPYQKKTQIEKLLEFMYGLNEKEVQLIFRLLYSDTKLN \r\nIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGRKGRPIYVYYVDREQLFKRISRD \r\nLEELVQASIAKLKEYIFKS", "organism": "Sulfolobus acidocaldarius", "uniprot_code": "Q4J9G1", "uniprot_range_first": 1, "uniprot_range_last": 123, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "METVLQIPYQKKTQIEKLLEFMYGLNEKEVQLIFRLLYSDTKLNIEELAEEFKVSKALIS\nKSLSELANKGLIEREKVSNEGRKGRPIYVYYVDREQLFKRISRDLEELVQASIAKLKEYI\nFKS", "mw": 16.368, "total_mw": 32.736, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "300 mM NaCl, 20 mM HEPES, pH 7.5", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Marburg, Germany", "full_name": "University of Marburg", "webpage": "http://www.uni-marburg.de/" } ], "contributor_name": "Marian", "contributor_surname": "Vogt", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-11-05", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.124, "sample_detector_distance": null, "concentration_min": null, "concentration_max": 0.63, "sample_volume": null, "flow_rate": null, "s_min": 0.035, "s_max": 4.944, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDG3_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDG3_fit1_model1.pdb", "model_mw": null, "bead_radius": 2.7, "log": "https://www.sasbdb.org/media/log_files/Dammif_P1_slow_Saci12230446p_merged029_030-10.log", "symmetry": null, "comment": null, "user": 255 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDG3_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.278, "p_value": 0.0, "fit_residual_plot": "SASDDG3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDG3_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammif_P1_slow_Saci12230446p_merged029_030-10.log", "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDG3_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDG3_fit2_model1.pdb", "model_mw": null, "bead_radius": 2.7, "log": "https://www.sasbdb.org/media/log_files/Dammif_P2_slow_Saci12230446p_merged029_030-8-1.pdb", "symmetry": null, "comment": null, "user": 255 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDG3_fit2_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.34, "p_value": 1.3e-05, "fit_residual_plot": "SASDDG3_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDG3_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammif_P2_slow_Saci12230446p_merged029_030-8.log", "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Archaeal biofilm regulator 2 (AbfR2) in complex with 40 base-pair dsDNA (Sa0446 binding sequence) in 300 mM NaCl, 20 mM HEPES, pH 7.5, were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.63 mg/ml was measured at 4°C. 10 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.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 41.981, "experimental_mw_error": null, "guinier_i0_mw": 67.74, "guinier_i0_mw_error": 0.0, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 68.09, "pddf_i0_error": null, "guinier_i0": 67.74, "guinier_i0_error": 0.17, "pddf_rg": 3.561, "pddf_rg_error": null, "guinier_rg": 3.44, "guinier_rg_error": 0.81, "pddf_dmax": 12.8, "pddf_dmax_error": null, "porod_volume": 60.38, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 18, "guinier_point_last": 64, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDG3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }