{ "code": "SASDYV3", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system", "publication": { "title": "Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system", "author_list": "Rodriguez C, Audette G", "journal": "Structural Dynamics", "doi": "10.1063/4.0001201", "pmid": null, "published_date": "2026 Mar 17" }, "status": "released", "submitted_date": "2025-12-10", "released_date": "2026-03-18" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDYV3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDYV3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDYV3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDYV3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDYV3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDYV3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDYV3.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger2 XE 9M", "resolution": 72.0 }, "name": "Advanced Photon Source (APS), Argonne National Laboratory", "city": "Lemont, IL", "country": "USA", "beamline_name": "BioCAT 18ID", "beam_geometry": null, "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": "TraW (Δ1-18)", "short_name": null, "sequence": "MADLGTWGDLWPVKEPDMLTVIMQRLTALEQSGEMGRKMDAFKERVIRNSLRPPAVPGIGRTEKYGSRLFDPSVRLAADIRDNEGRVFARQGEVMNPLQYVPFNQTLYFINGDDPAQVAWMKRQTPPTLESKIILVQGSIPEMQKSLDSRVYFDQNGVLCQRLGIDQVPARVSAVPGDRFLKVEFIPAEEGRK", "organism": "Escherichia coli (strain K12)", "uniprot_code": "P18472", "uniprot_range_first": 19, "uniprot_range_last": 210, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MRCRGLIALLIWGQSVAAADLGTWGDLWPVKEPDMLTVIMQRLTALEQSGEMGRKMDAFK\nERVIRNSLRPPAVPGIGRTEKYGSRLFDPSVRLAADIRDNEGRVFARQGEVMNPLQYVPF\nNQTLYFINGDDPAQVAWMKRQTPPTLESKIILVQGSIPEMQKSLDSRVYFDQNGVLCQRL\nGIDQVPARVSAVPGDRFLKVEFIPAEEGRK", "mw": 25.8, "total_mw": 25.8, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM HEPES, 100 mM NaCl, 5% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Conjugative protein of the F plasmid Type IV Secretion System, TraW.", "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": "York University", "webpage": null } ], "contributor_name": "Christina", "contributor_surname": "Rodriguez", "orcid": "https://orcid.org/0000-0002-1737-3976" } ], "concentration_method": null, "concentration_unit": null, "date": "2022-02-23", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 0.5, "number_of_frames": 2582, "wavelength": 0.1033, "sample_detector_distance": 3.7, "concentration_min": null, "concentration_max": 7.0, "sample_volume": 300.0, "flow_rate": 0.6, "s_min": 0.028, "s_max": 4.163, "total_exposure_time": null, "seccolumn": 1 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDYV3_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/SASDYV3_fit1_model1.cif", "model_mw": null, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/refine_WTBM_902.log", "symmetry": null, "comment": null, "user": 1301 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDYV3_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.127, "p_value": 0.7558, "fit_residual_plot": "SASDYV3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDYV3_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_WTBM_902.log", "software_version": "3.2.1", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "3.2.1", "i0_calibration_standard": null, "description": "Synchrotron SAXS data from solutions of TraW in 20 mM HEPES, 100 mM NaCl, 5% glycerol, pH 7 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS; Argonne National Laboratory USA) using a Eiger2 XE 9M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.1033 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 300.00 μl sample at 7 mg/ml was injected at a 0.6 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 2582 successive 0.500 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.", "experiment_description": null, "tags": [], "intensity_unit": null, "experimental_mw": 25.7, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 25.7, "porod_mw_error": null, "pddf_i0": 0.5917, "pddf_i0_error": 0.0016, "guinier_i0": 0.00618784, "guinier_i0_error": null, "pddf_rg": 2.63, "pddf_rg_error": 0.015, "guinier_rg": 2.63, "guinier_rg_error": 0.646, "pddf_dmax": 9.0, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 26, "guinier_point_last": 240, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDYV3_datloglog_img.png", "symmetry": null, "last_modified": "2026-03-18T13:59:43.788484+01:00", "bragg_peak": [] }