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{
"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": []
}
