The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDC45",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules.",
"publication": {
"title": "Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules.",
"author_list": "Paxman JJ, Lo AW, Sullivan MJ, Panjikar S, Kuiper M, Whitten AE, Wang G, Luan CH, Moriel DG, Tan L, Peters KM, Phan MD, Gee CL, Ulett GC, Schembri MA, Heras B",
"journal": "Nat Commun",
"doi": "10.1038/s41467-019-09814-6",
"pmid": "31036849",
"published_date": "2019 Apr 29"
},
"status": "released",
"submitted_date": "2017-06-16",
"released_date": "2019-03-29"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC45.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC45.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC45_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC45_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC45_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC45_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC45.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 autotransporter protein UpaB",
"short_name": "Alpha-UpaB",
"sequence": "SNATDSTVSTDPVTLNTEKTTLDQDVVINGDNKITAVTIETSDSDKDLNVTFGGHDITAASTVNQDFVEGVKVSGNKNVVINATDSTITAQGEGTYVRTAMVIDSTGDVVVNGGNFVAKNEKGSATGISLEATTGNNLTLNGTTINAQGNKSYSNGSTAIFAQKGNLLQGFDGDATDNITLADSNIINGGIETIVTAGNKTGIHTVNLNIKDGSVIGAANNKQTIYASASAQGAGSATQNLNLSVADSTIYSDVLALSESENSASTTTNVNMNVARSYWEGNAYTFNSGDKAGSDLDINLSDSSVWKGKVSGAGDASVSLQNGSVWNVTGSSTVDALAVKDSTVNITKATVNTGTFASQNGTLIVDASSENTLDISGKASGDLRVYSAGSLDLINEQTAFISTGKDSTLKATGTTEGGLYQYDLTQGADGNFYFVKNTHKASNASSVIQAMAAAPANVANLQADTL",
"organism": "E. Coli CFT073",
"uniprot_code": "A0A0H2V5A3",
"uniprot_range_first": 37,
"uniprot_range_last": 500,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKLVTRMENFFMKNSKVFYRSALATAIVMALSAPAFATDSTVSTDPVTLNTEKTTLDQDV\nVINGDNKITAVTIETSDSDKDLNVTFGGHDITAASTVNQDFVEGVKVSGNKNVVINATDS\nTITAQGEGTYVRTAMVIDSTGDVVVNGGNFVAKNEKGSATGISLEATTGNNLTLNGTTIN\nAQGNKSYSNGSTAIFAQKGNLLQGFDGDATDNITLADSNIINGGIETIVTAGNKTGIHTV\nNLNIKDGSVIGAANNKQTIYASASAQGAGSATQNLNLSVADSTIYSDVLALSESENSAST\nTTNVNMNVARSYWEGNAYTFNSGDKAGSDLDINLSDSSVWKGKVSGAGDASVSLQNGSVW\nNVTGSSTVDALAVKDSTVNITKATVNTGTFASQNGTLIVDASSENTLDISGKASGDLRVY\nSAGSLDLINEQTAFISTGKDSTLKATGTTEGGLYQYDLTQGADGNFYFVKNTHKASNASS\nVIQAMAAAPANVANLQADTLSARQDAVRLSENDKGGVWIQYFGGKQKHTTAGNASYDLDV\nNGVMLGGDTRFMTEDGSWLAGVAMSSAKGDMTTMQSKGDTEGYSFHAYLSRQYNNGIFID\nTAAQFGHYSNTADVRLMNGGGTIKADFNTNGFGAMVKGGYTWKDGNGLFIQPYAKLSALT\nLEGVDYQLNGVDVHSDSYNSVLGEAGTRVGYDFAVGNATVKPYLNLAALNEFSDGNKVRL\nGDESVNASIDGAAFRVGAGVQADITKNMGAYASLDYTKGDDIENPLQGVVGINVTW",
"mw": 47.673,
"total_mw": 47.673,
"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": "Alpha domain of autotransporter protein UpaB from UPEC",
"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": "2015-05-01",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 35,
"wavelength": 0.1033,
"sample_detector_distance": 1.428,
"concentration_min": 0.1,
"concentration_max": 2.7,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.114,
"s_max": 2.998,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC45_fit1_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.8.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC45_fit1_model1.pdb",
"model_mw": 49.397,
"bead_radius": 2.5,
"log": "https://www.sasbdb.org/media/log_files/damsel.log",
"symmetry": "P1",
"comment": "",
"user": 111
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC45_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.468,
"p_value": 0.021,
"fit_residual_plot": "SASDC45_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC45_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run0.log",
"software_version": "5.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC45_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "6bea",
"ext_code": "6BEA",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "1.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC45_fit2_model1.pdb",
"model_mw": 47.97,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/run5.log",
"symmetry": "P1",
"comment": "Coral was used to model residues from the N-terminus and C-terminus missing from the PDB model",
"user": 111
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC45_fit2_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.77,
"p_value": 0.0,
"fit_residual_plot": "SASDC45_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC45_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run5.log",
"software_version": "1.1",
"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 solutions of the alpha domain of the autotransporter protein UpaB from uropathogenic E. coli (UPEC) in 25 mM HEPES 150mM NaCl pH 7.5 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) 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=0.1033 nm). Thirty five successive 1 second frames were collected across solute concentrations of 0.1-2.7 mg/ml. The SAXS data displayed this entry was derived from a 0.7 mg/ml sample. 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 rigid-body modelling using CORAL (bottom).",
"tags": [],
"intensity_unit": null,
"experimental_mw": 46.7,
"experimental_mw_error": null,
"guinier_i0_mw": 46.7,
"guinier_i0_mw_error": 2.5,
"porod_mw": 54.1,
"porod_mw_error": null,
"pddf_i0": 0.0271,
"pddf_i0_error": 5e-05,
"guinier_i0": 0.0271,
"guinier_i0_error": 6e-05,
"pddf_rg": 2.97,
"pddf_rg_error": 0.01,
"guinier_rg": 2.93,
"guinier_rg_error": 0.01,
"pddf_dmax": 10.5,
"pddf_dmax_error": 0.5,
"porod_volume": 66.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 41,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDC45_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-11-11T19:36:14.286041+01:00",
"bragg_peak": []
}
