{ "code": "SASDF33", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Inhibition of aggregation and biofilm formation by Uropathogenic Escherichia coli", "publication": null, "status": "released", "submitted_date": "2019-02-14", "released_date": "2024-02-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF33.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF33.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF33_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF33_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF33_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF33_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF33.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "SAXS/WAXS", "beam_geometry": "Point", "type_of_source": "X-ray synchrotron", "point_source": true, "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": "Alpha domain of Ag43a", "short_name": "Ag43", "sequence": "ADIVVHPGETVNGGTLVNHDNQFVSGTANGVTVSTGLELGPDSDENTGGQWIKAGGTGRNTTVTANGRQIVQAGGTASDTVIRDGGGQSLNGLAVNTTLDNRGEQWVHGGGKAAGTIINQDGYQTIKHGGLATGTIVNTGAESSGQMVGGTAESTTINKNGRQVIWSSGMARDTLIYAGGDQTVHGEAHNTRLEGGNQYVHNGGTATETLINRDGWQVIKEGGTAAHTTINQKGKLQVNAGGKASDVTQNTGGALVTSTAATVTGTNRLGAFSVVAGKADNVVLENGGRLDVLSGHTATNTRVDDGGTLDIRNGGAATTVSMGNGGVLLADSGAAVSGTRSDGKAFSIGGGQADALMLEKGSSFTLNAGDTATDTTVNGGLFTARGGTLAGTTTLNNGAILTLSGKTVNNDTLTIREGDALLQGGSLTGNGSVEKSGSGTLTVSNTTLTQKAVNLNEGTLTLNDSTVTTDVIAQRGTALKLTGSTVLNGAID", "organism": "Escherichia coli", "uniprot_code": "P39180", "uniprot_range_first": 53, "uniprot_range_last": 551, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 49.087, "total_mw": 49.087, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Fragment antigen-binding region Fab10C12", "short_name": "Fab10C12", "sequence": "SIVMTQTPKFLFVSVGDRVTITCKASQSVNNDVAWYQQKPGQSPKLLIYFASNRYTGVPDRFTGSGYGTDFTFTINTVQAEDLAVYFCQQDYSSPQTFGGGTKLEVTRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC \r\nQVQLQQPGTELVKPGASVKLSCKASGYTFTNYWMHWVKQRPGQGLEWIGNIGPSSGNTNYGENFKTKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGSIRAMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKL", "organism": "Mus musculus", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 46.565, "total_mw": 46.565, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM HEPES, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Antigen 43/Fragment antigen-binding region Fab10C12 complex (Ag43-Fab)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "ANSTO", "address": "Kirrawee DC, NSW 2232, Australia", "full_name": "Australian Nuclear Science and Technology Organisation", "webpage": "" } ], "contributor_name": "Andrew", "contributor_surname": "Whitten", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-11-03", "storage_temperature": 4.0, "cell_temperature": 12.0, "exposure_time": 1.0, "number_of_frames": 14, "wavelength": 0.10332, "sample_detector_distance": 2.68, "concentration_min": 0.25, "concentration_max": 1.2, "sample_volume": null, "flow_rate": null, "s_min": 0.088, "s_max": 2.989, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF33_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF33_fit1_model1.pdb", "model_mw": 69.176, "bead_radius": 3.25, "log": null, "symmetry": "P1", "comment": null, "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF33_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.215, "p_value": 0.381566, "fit_residual_plot": "SASDF33_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF33_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run12.log", "software_version": "5.3", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF33_fit2_model1_img.png", "software": "Custom in-house", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF33_fit2_model1.pdb", "model_mw": 91.42, "bead_radius": null, "log": null, "symmetry": "P1", "comment": null, "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF33_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 3.357, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF33_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Ag43Fab101.log", "software_version": "2.8.3", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "X-ray synchrotron radiation scattering data from the from the Ag43-Fab complex in 25 mM HEPES 150mM NaCl pH 7.0 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) in a SEC-SAXS with sheath flow configuration using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.10332 nm). Approximately 50 uL of a 5.0 mg/ml protein solution was injected onto a S200 Increase 5/150 column at a flow rate of 0.4 ml/min. Three hundred successive 1 second frames were collected during the SEC-SAXS run. The peak of the elution profile occured at ~3 mins after the start of the run, and the protein scattering was taken as the average of 14 frames collected 190-203 seconds after the peak eluted. The concentration range corresponding to the averaged frames was ~0.25 - 1.20 mg/ml, and the average concentration was taken as ~0.59 mg/ml. The buffer was taken as the sum of 50 frames collected between 1-2 mins after the start of the run. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN (top) and CRYSOL using the crystal structure (bottom).", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 92.0, "experimental_mw_error": null, "guinier_i0_mw": 92.0, "guinier_i0_mw_error": 5.0, "porod_mw": 85.0, "porod_mw_error": null, "pddf_i0": 0.02158, "pddf_i0_error": null, "guinier_i0": 0.02173, "guinier_i0_error": 8e-05, "pddf_rg": 4.28, "pddf_rg_error": null, "guinier_rg": 4.29, "guinier_rg_error": 0.04, "pddf_dmax": 15.0, "pddf_dmax_error": null, "porod_volume": 103.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 14, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF33_datloglog_img.png", "symmetry": null, "last_modified": "2024-02-21T18:31:10.310547+01:00", "bragg_peak": [] }