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": "SASDCK2",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"publication": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"author_list": "Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE",
"journal": "Acta Crystallogr D Struct Biol",
"doi": "10.1107/S2059798317011597",
"pmid": "28876235",
"published_date": "2017 Sep 1"
},
"status": "released",
"submitted_date": "2017-05-06",
"released_date": "2017-08-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCK2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCK2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCK2.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": "Xylose isomerase",
"short_name": "Glucose Isomerase",
"sequence": "MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\r\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\r\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\r\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\r\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\r\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\r\nDVDAAAARGMAFERLDQLAMDHLLGARG",
"organism": "Streptomyces rubiginosus",
"uniprot_code": "P24300",
"uniprot_range_first": 1,
"uniprot_range_last": 388,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\nDVDAAAARGMAFERLDQLAMDHLLGARG",
"mw": 43.227,
"total_mw": 172.908,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3",
"concentration_unit": null,
"comment": "2 mM TCEP and 0.1% (.01538 M) NaN3 used for radiation protection",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Glucose Isomerase - Streptomyces rubiginosus",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Sydney, New South Wales 2006, Australia",
"full_name": "School of Molecular Bioscience, University of Sydney.",
"webpage": ""
}
],
"contributor_name": "Jill",
"contributor_surname": "Trewhella",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-03-09",
"storage_temperature": null,
"cell_temperature": 22.0,
"exposure_time": 1.0,
"number_of_frames": 24,
"wavelength": 0.10332,
"sample_detector_distance": 2.683,
"concentration_min": 0.06,
"concentration_max": 0.34,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.066,
"s_max": 3.104,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK2_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "on-line",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK2_fit1_model1.pdb",
"model_mw": 120.74,
"bead_radius": 2.4,
"log": "https://www.sasbdb.org/media/log_files/GIstderr.log",
"symmetry": "P1",
"comment": "job submitted ATSAS on-line April 9, 2017",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.951,
"p_value": 0.035,
"fit_residual_plot": "SASDCK2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/GIstderr.log",
"software_version": "on-line",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/GI_tet_img.png",
"software": "FoXS",
"pdb_link": [
{
"pdb_code": "1oad",
"ext_code": "1OAD",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "on-line",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK2_fit2_model1.pdb",
"model_mw": 173.7,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "GI tetramer generated from PDB:1OAD using symmetry transforms in pymol",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit2_fitfoxs_img.png",
"software": "FoXS",
"chi_square_value": 1.02,
"p_value": 0.045511,
"fit_residual_plot": "SASDCK2_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK2_fit2.dat",
"fit_log": null,
"software_version": "on-line",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of glucoes isomerase in 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3, pH 7.5 were collected on the SAXS/WAXS beam line at Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Scattering data are on an absolute scale (cm-1) set by reference to the scattering from pure H2O. I(0) values must be corrected for the shear flow sample cell by a 2.05 multiplicative factor. Data were acquired in SEC-SAXS mode, summed from 21 measurement frames where Rg was flat and at a maximum. The average concentration over the frames was 0.18 mg/mL, spanning values from 0.06 - 0.34 mg/mL. Sample concentrations were measured by A280 (extinction coefficient for 1 mg/mL, 10 mm pathlength; E0.1% = 1.079), corrected for the 3.1 mm path-length of the UV measurement cell. MULCh was used to calculate the partial specific volume (0.732 mL/g) and X-ray contrast (Δρ = 2.833e10 cm-2). The protein is a tetramer in the solution conditions measured.",
"tags": [
"benchmark"
],
"intensity_unit": "1/cm",
"experimental_mw": 172.234,
"experimental_mw_error": null,
"guinier_i0_mw": 183.254,
"guinier_i0_mw_error": null,
"porod_mw": 152.667,
"porod_mw_error": null,
"pddf_i0": 0.03739,
"pddf_i0_error": 3.9e-05,
"guinier_i0": 0.037,
"guinier_i0_error": 4.4e-05,
"pddf_rg": 3.265,
"pddf_rg_error": 0.004,
"guinier_rg": 3.287,
"guinier_rg_error": 0.013,
"pddf_dmax": 9.22,
"pddf_dmax_error": null,
"porod_volume": 229.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 43,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCK2_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-03-08T11:32:18.321280+01:00",
"bragg_peak": []
}
