{ "code": "SASDDC9", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.", "publication": { "title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.", "author_list": "Kutnowski N, Shmuely H, Dahan I, Shmulevich F, Davidov G, Shahar A, Eichler J, Zarivach R, Shaanan B", "journal": "J Struct Biol", "doi": "10.1016/j.jsb.2018.08.008", "pmid": "30110657", "published_date": "2018 Aug 12" }, "status": "released", "submitted_date": "2018-06-29", "released_date": "2018-08-15" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDC9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDC9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDC9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDC9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDC9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDC9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDC9.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": "VNG0258H/RosR", "short_name": "VNG0258H/RosR", "sequence": ">VNG0258H/RosR\r\nMSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDL\r\nVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADDAAAL\r\nEHHHHHH", "organism": "Halobacterium salinarum NRC-1", "uniprot_code": "Q9HSF4", "uniprot_range_first": 1, "uniprot_range_last": 116, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDL\nVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADD", "mw": 14.533, "total_mw": 29.066, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES, 2 M RbCl, 0.02% NaN3", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Structure of Halobacterium salinarum VNG0258H/RosR in the presence of 2 M RbCl", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Israel", "full_name": "Ben-Gurion University of the Negev", "webpage": "https://in.bgu.ac.il/" } ], "contributor_name": "Nitzan", "contributor_surname": "kutnowski", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2015-03-07", "storage_temperature": 25.0, "cell_temperature": 25.0, "exposure_time": 2.0, "number_of_frames": 10, "wavelength": 0.09919, "sample_detector_distance": 2.864, "concentration_min": null, "concentration_max": 5.1, "sample_volume": null, "flow_rate": null, "s_min": 0.034, "s_max": 4.975, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDC9_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDC9_fit1_model1.pdb", "model_mw": 39.36, "bead_radius": 3.3, "log": null, "symmetry": null, "comment": null, "user": 339 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/2M_RbCl_SASDDC9_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5", "model_data": "https://www.sasbdb.org/media/pdb_file/2M_RbCl_SASDDC9.pdb", "model_mw": 31.79, "bead_radius": 2.0, "log": null, "symmetry": null, "comment": null, "user": 339 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDC9_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.225272, "p_value": 0.442257, "fit_residual_plot": "SASDDC9_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDC9_fit1.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": "Individual (top) and spatially averaged (DAMFILT, bottom) ab initio models are displayed.", "experiment_description": "Synchrotron SAXS data from solutions of Halobacterium salinarum VNG0258H/RosR in 50 mM HEPES, 2 M RbCl, 0.02% NaN3, pH 7 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.10 mg/ml was measured at 25°C. 10 successive 2 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": null, "experimental_mw": 42.26, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 55.0, "porod_mw_error": null, "pddf_i0": 12.26, "pddf_i0_error": 0.05, "guinier_i0": 13.04, "guinier_i0_error": 0.056, "pddf_rg": 3.1, "pddf_rg_error": 0.01, "guinier_rg": 3.28, "guinier_rg_error": 0.43, "pddf_dmax": 9.3, "pddf_dmax_error": null, "porod_volume": 89.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 29, "guinier_point_last": 77, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDC9_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }