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{
"code": "SASDFK3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ.",
"publication": {
"title": "A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ.",
"author_list": "Hewage TW, Caria S, Lee M",
"journal": "Acta Crystallogr F Struct Biol Commun",
"doi": "10.1107/S2053230X19006599",
"pmid": "31204691",
"published_date": "2019 Jun 1"
},
"status": "released",
"submitted_date": "2019-02-28",
"released_date": "2019-05-27"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFK3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFK3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFK3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFK3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFK3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFK3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFK3.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": "Splicing factor, proline- and glutamine-rich",
"short_name": "SFPQ",
"sequence": "GAMEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFG\r\nFIKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFG\r\nPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDD\r\nEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDA\r\nKDKLESEMEDAYHEHQANLL",
"organism": "Homo sapiens",
"uniprot_code": "P23246",
"uniprot_range_first": 276,
"uniprot_range_last": 535,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSRDRFRSRGGGGGGFHRRGGGGGRGGLHDFRSPPPGMGLNQNRGPMGPGPGQSGPKPPI\nPPPPPHQQQQQPPPQQPPPQQPPPHQPPPHPQPHQQQQPPPPPQDSSKPVVAQGPGPAPG\nVGSAPPASSSAPPATPPTSGAPPGSGPGPTPTPPPAVTSAPPGAPPPTPPSSGVPTTPPQ\nAGGPPPPPAAVPGPGPGPKQGPGPGGPKGGKMPGGPKPGGGPGLSTPGGHPKPPHRGGGE\nPRGGRQHHPPYHQQHHQGPPPGGPGGRSEEKISDSEGFKANLSLLRRPGEKTYTQRCRLF\nVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGR\nQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFAS\nKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRF\nAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLLRQDLM\nRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQREESYSRM\nGYMDPRERDMRMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVPPATMSGSMMGS\nDMRTERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF",
"mw": 30.049,
"total_mw": 60.098,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl, 250 mM NaCl, 5% (v/v) glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Splicing factor, proline- and glutamine-rich (SFPQ)",
"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": "Sofia",
"contributor_surname": "Caria",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-04-19",
"storage_temperature": null,
"cell_temperature": 25.0,
"exposure_time": 1.0,
"number_of_frames": 4,
"wavelength": 0.10332,
"sample_detector_distance": 2.68,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.088,
"s_max": 3.518,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFK3_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "4wii",
"ext_code": "4wii",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFK3_fit1_model1.pdb",
"model_mw": 60.28,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 123
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SFPQ_P212121_dimer_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.108,
"p_value": 8.7e-05,
"fit_residual_plot": "fit4columns2300_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFK3_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFK3_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "6ncq",
"ext_code": "6NCQ",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFK3_fit2_model1.pdb",
"model_mw": 60.11,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 123
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SFPQ_C2221_dimer_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.256,
"p_value": 0.011216,
"fit_residual_plot": "SFPQ_C2221_dimer_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFK3_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5",
"i0_calibration_standard": null,
"description": "CORAL was used to compare the scattering profile against the two PDB models of SFPQ in either P212121 or C2221 crystallographic space groups (CRYSOL fits to the data are shown; Coral models and fits are included in the full entry zip archive).",
"experiment_description": "Synchrotron SAXS data from solutions of SFPQ in 20 mM Tris-HCl, 250 mM NaCl, 5% (v/v) glycerol, pH 7.5 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 2-1M detector at a sample-detector distance of 2.68 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Data was collected in an in-line SEC-SAXS experimental setup coupled to a co-flow sample sheath flow environment run at a fractional sample flow rate of 0.5 mL/min at 25°C. The protein complex was analysed after size exclusion chromatography using a Superdex 200 5/150 column (45μl of sample injected at 5mg/ml). The low angle data collected were obtained from a single scattering curve obtained by selecting data from the peak with highest intensity and consistent Rg. Given that coflow was used for the measurements, the I(0) here presented was corrected by a factor 2.05 (original I(0) is 0.059). The data presented corresponds to a two standard errors.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 60.58,
"experimental_mw_error": null,
"guinier_i0_mw": 60.58,
"guinier_i0_mw_error": null,
"porod_mw": 57.0,
"porod_mw_error": null,
"pddf_i0": 0.05871,
"pddf_i0_error": 0.00016,
"guinier_i0": 0.05911,
"guinier_i0_error": 0.00016,
"pddf_rg": 2.731,
"pddf_rg_error": 0.008,
"guinier_rg": 2.77,
"guinier_rg_error": 0.01,
"pddf_dmax": 8.2,
"pddf_dmax_error": null,
"porod_volume": 91.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 106,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFK3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
