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": "SASDFB6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Protease-associated import systems are widespread in Gram-negative bacteria.",
"publication": {
"title": "Protease-associated import systems are widespread in Gram-negative bacteria.",
"author_list": "Grinter R, Leung PM, Wijeyewickrema LC, Littler D, Beckham S, Pike RN, Walker D, Greening C, Lithgow T",
"journal": "PLoS Genet",
"doi": "10.1371/journal.pgen.1008435",
"pmid": "31613892",
"published_date": "2019 Oct"
},
"status": "released",
"submitted_date": "2019-05-08",
"released_date": "2019-09-24"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFB6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFB6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFB6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFB6.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": "Zinc protease PqqL",
"short_name": null,
"sequence": "AALPQDEKLITGQLDNGLRYMIYPHAHPKDQVNL\r\nWLQIHTGSLQEEDNELGVAHFVEHMMFNGTKTWPGNKVIETFESMGLRFGRDVNAYTSYD\r\nETVYQVSLPTTQKQNLQQVMAIFSEWSNAATFEKLEVDAERGVITEEWRAHQDAKWRTSQ\r\nARRPFLLANTRNLDREPIGLMDTVATVTPAQLRQFYQRWYQPNNMTFIVVGDIDSKEALA\r\nLIKDNLSKLPANKAAENRVWPTKAENHLRFNIINDKENRVNGIALYYRLPMVQVNDEQSF\r\nIEQAEWSMLVQLFNQRLQERIQSGELKTISGGTARSVKIAPDYQSLFFRVNARDDNMQDA\r\nANALMAELATIDQHGFSAEELDDVKSTRLTWLKNAVDQQAERDLRMLTSRLASSSLNNTP\r\nFLSPEETYQLSKRLWQQITVQSLAEKWQQLRKNQDAFWEQMVNNEVAAKKALSPAAILAL\r\nEKEYANKKLAAYVFPGRNLSLTVDADPQAEISSKETLAENLTSLTLSNGARVILAKSAGE\r\nEQKLQIIAVSNKGDLSFPAQQKSLIALANKAVSGSGVGELSSSSLKRWSAENSVTMSSKV\r\nSGMNTLLSVSARTNNPEPGFQLINQRITHSTINDNIWASLQNAQIQALKTLDQRPAEKFA\r\nQQMYETRYADDRTKLLQENQIAQFTAADALAADRQLFSSPADITFVIVGNVAEDKLVALI\r\nTRYLGSIKHSDSPLAAGKPLTRATDNASVTVKEQNEPVAQVSQWKRYDSRTPVNLPTRMA\r\nLDAFNVALAKDLRVNIREQASGAYSVSSRLSVDPQAKDISHLLAFTCQPERHDELLTLAN\r\nEVMVKRLAKGISEQELNEYQQNVQRSLDIQQRSVQQLANTIVNSLIQYDDPAAWTEQEQL\r\nLKQMTVENVNTAVKQYLSHPVNTYTGVLLPK",
"organism": "Escherichia coli",
"uniprot_code": "P31828",
"uniprot_range_first": 27,
"uniprot_range_last": 931,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MEIIMRNLCFLLTLVATLLLPGRLIAAALPQDEKLITGQLDNGLRYMIYPHAHPKDQVNL\nWLQIHTGSLQEEDNELGVAHFVEHMMFNGTKTWPGNKVIETFESMGLRFGRDVNAYTSYD\nETVYQVSLPTTQKQNLQQVMAIFSEWSNAATFEKLEVDAERGVITEEWRAHQDAKWRTSQ\nARRPFLLANTRNLDREPIGLMDTVATVTPAQLRQFYQRWYQPNNMTFIVVGDIDSKEALA\nLIKDNLSKLPANKAAENRVWPTKAENHLRFNIINDKENRVNGIALYYRLPMVQVNDEQSF\nIEQAEWSMLVQLFNQRLQERIQSGELKTISGGTARSVKIAPDYQSLFFRVNARDDNMQDA\nANALMAELATIDQHGFSAEELDDVKSTRLTWLKNAVDQQAERDLRMLTSRLASSSLNNTP\nFLSPEETYQLSKRLWQQITVQSLAEKWQQLRKNQDAFWEQMVNNEVAAKKALSPAAILAL\nEKEYANKKLAAYVFPGRNLSLTVDADPQAEISSKETLAENLTSLTLSNGARVILAKSAGE\nEQKLQIIAVSNKGDLSFPAQQKSLIALANKAVSGSGVGELSSSSLKRWSAENSVTMSSKV\nSGMNTLLSVSARTNNPEPGFQLINQRITHSTINDNIWASLQNAQIQALKTLDQRPAEKFA\nQQMYETRYADDRTKLLQENQIAQFTAADALAADRQLFSSPADITFVIVGNVAEDKLVALI\nTRYLGSIKHSDSPLAAGKPLTRATDNASVTVKEQNEPVAQVSQWKRYDSRTPVNLPTRMA\nLDAFNVALAKDLRVNIREQASGAYSVSSRLSVDPQAKDISHLLAFTCQPERHDELLTLAN\nEVMVKRLAKGISEQELNEYQQNVQRSLDIQQRSVQQLANTIVNSLIQYDDPAAWTEQEQL\nLKQMTVENVNTAVKQYLSHPVNTYTGVLLPK",
"mw": 101.744,
"total_mw": 101.744,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris HCl, 150 nM NaCl, 0.02 % NaN3, 5% glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.8,
"deuteration": null
},
"purity_method": null,
"name": "The periplasmically localised protease PqqL from Escherichia coli",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Melbourne, Australia",
"full_name": "Monash University",
"webpage": "http://www.monash.edu/"
}
],
"contributor_name": "Grinter",
"contributor_surname": "Grinter",
"orcid": "https://orcid.org/0000-0002-8195-5348"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-06-14",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.10322,
"sample_detector_distance": 1.426,
"concentration_min": null,
"concentration_max": 8.0,
"sample_volume": 100.0,
"flow_rate": 0.4,
"s_min": 0.057,
"s_max": 3.188,
"total_exposure_time": null,
"seccolumn": 2
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit1_model1.pdb",
"model_mw": 116.37,
"bead_radius": 3.5,
"log": "https://www.sasbdb.org/media/log_files/PqqL_sub_sca_avg2-1.log",
"symmetry": null,
"comment": null,
"user": 322
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit1_model2_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit1_model2.pdb",
"model_mw": 116.37,
"bead_radius": 3.5,
"log": "https://www.sasbdb.org/media/log_files/PqqL_sub_sca_avg2-1_cXdQQnM.log",
"symmetry": "P1",
"comment": null,
"user": 322
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PqqL_sub_sca_avg2-1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.506,
"p_value": 0.003869,
"fit_residual_plot": "PqqL_sub_sca_avg2-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFB6_fit1.fir",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6ofs",
"ext_code": "6OFS",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit2_model1.pdb",
"model_mw": 101.9,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/PqqL_FL_refine.log",
"symmetry": "P1",
"comment": null,
"user": 322
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PqqL_FL_refine_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 9.541,
"p_value": 0.0,
"fit_residual_plot": "PqqL_FL_refine_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFB6_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/PqqL_FL_refine.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of periplasmically localised protease (PqqL) from E. coli in 20 mM Tris HCl, 150 nM NaCl, 0.02 % NaN3, 5% glycerol, pH 7.8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.4 m and at a wavelength of λ = 0.10322 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed using a co-flow apparatus. The SEC parameters were as follows: A 100 μl sample at 8 mg/ml was injected onto a GE Superdex 200 Increase 5/150 column at 20°C. 10 successive 1 second frames were collected through the SEC elution peak. 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": "arbitrary",
"experimental_mw": 113.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 130.0,
"porod_mw_error": null,
"pddf_i0": 0.08263,
"pddf_i0_error": null,
"guinier_i0": 0.13678,
"guinier_i0_error": 0.0002,
"pddf_rg": 4.11,
"pddf_rg_error": null,
"guinier_rg": 4.02,
"guinier_rg_error": 0.88,
"pddf_dmax": 13.69,
"pddf_dmax_error": null,
"porod_volume": 207.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 70,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFB6_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
