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.
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{
"code": "SASDEJ6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth",
"publication": {
"title": "Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth",
"author_list": "Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M",
"journal": null,
"doi": "10.1101/464131",
"pmid": null,
"published_date": "2018 Nov 06"
},
"status": "released",
"submitted_date": "2018-10-16",
"released_date": "2019-06-19"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEJ6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEJ6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEJ6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEJ6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": "1 x 5 mm",
"type_of_source": "X-ray synchrotron",
"point_source": null,
"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": "Epstein-Barr nuclear antigen 2",
"short_name": "EBNA2 Type1",
"sequence": ">EBNA2_T1_381-455\r\nSMPELSPVLGLHQGQGAGDSPTPGPSNAAPVCRNSHTATPNVSPIHEPESHNSPEAPILFPDDWYPPSIDPADLD",
"organism": "Human gammaherpesvirus 4",
"uniprot_code": "P12978",
"uniprot_range_first": 381,
"uniprot_range_last": 455,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MPTFYLALHGGQTYHLIVDTDSLGNPSLSVIPSNPYQEQLSDTPLIPLTIFVGENTGVPP\nPLPPPPPPPPPPPPPPPPPPPPPPPPPPSPPPPPPPPPPPQRRDAWTQEPSPLDRDPLGY\nDVGHGPLASAMRMLWMANYIVRQSRGDRGLILPQGPQTAPQARLVQPHVPPLRPTAPTIL\nSPLSQPRLTPPQPLMMPPRPTPPTPLPPATLTVPPRPTRPTTLPPTPLLTVLQRPTELQP\nTPSPPRMHLPVLHVPDQSMHPLTHQSTPNDPDSPEPRSPTVFYNIPPMPLPPSQLPPPAA\nPAQPPPGVINDQQLHHLPSGPPWWPPICDPPQPSKTQGQSRGQSRGRGRGRGRGRGKGKS\nRDKQRKPGGPWRPEPNTSSPSMPELSPVLGLHQGQGAGDSPTPGPSNAAPVCRNSHTATP\nNVSPIHEPESHNSPEAPILFPDDWYPPSIDPADLDESWDYIFETTESPSSDEDYVEGPSK\nRPRPSIQ",
"mw": 7.831,
"total_mw": 15.662,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Zinc finger MYND domain-containing protein 11",
"short_name": "BS69 CC-MYND",
"sequence": ">BS69-CC-MYND\r\nDRMKSDHKRETERVVREALEKLRSEMEEEKRQAVNKAVANMQGEMDRKCKQVKEKCKEEFVEEIKKLATQHKQLISQTKKKQWCYNCEEEAMYHCCWNTSYCSIKCQQEHWHAEHKRTCRRKR",
"organism": "Homo sapiens",
"uniprot_code": "Q15326",
"uniprot_range_first": 480,
"uniprot_range_last": 602,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MARLTKRRQADTKAIQHLWAAIEIIRNQKQIANIDRITKYMSRVHGMHPKETTRQLSLAV\nKDGLIVETLTVGCKGSKAGIEQEGYWLPGDEIDWETENHDWYCFECHLPGEVLICDLCFR\nVYHSKCLSDEFRLRDSSSPWQCPVCRSIKKKNTNKQEMGTYLRFIVSRMKERAIDLNKKG\nKDNKHPMYRRLVHSAVDVPTIQEKVNEGKYRSYEEFKADAQLLLHNTVIFYGADSEQADI\nARMLYKDTCHELDELQLCKNCFYLSNARPDNWFCYPCIPNHELVWAKMKGFGFWPAKVMQ\nKEDNQVDVRFFGHHHQRAWIPSENIQDITVNIHRLHVKRSMGWKKACDELELHQRFLREG\nRFWKSKNEDRGEEEAESSISSTSNEQLKVTQEPRAKKGRRNQSVEPKKEEPEPETEAVSS\nSQEIPTMPQPIEKVSVSTQTKKLSASSPRMLHRSTQTTNDGVCQSMCHDKYTKIFNDFKD\nRMKSDHKRETERVVREALEKLRSEMEEEKRQAVNKAVANMQGEMDRKCKQVKEKCKEEFV\nEEIKKLATQHKQLISQTKKKQWCYNCEEEAMYHCCWNTSYCSIKCQQEHWHAEHKRTCRR\nKR",
"mw": 15.064,
"total_mw": 60.256,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Brighton, UK",
"full_name": "University of Sussex",
"webpage": "http://www.sussex.ac.uk/"
}
],
"contributor_name": "Rajesh",
"contributor_surname": "Ponnusamy",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-11-29",
"storage_temperature": 4.0,
"cell_temperature": 25.0,
"exposure_time": 3.0,
"number_of_frames": 25,
"wavelength": 0.1,
"sample_detector_distance": 4.014,
"concentration_min": null,
"concentration_max": 9.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.103,
"s_max": 2.417,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEJ6_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEJ6_fit1_model1.pdb",
"model_mw": 52.65,
"bead_radius": 3.0,
"log": "https://www.sasbdb.org/media/log_files/E2T1-BS69-483-507.log",
"symmetry": null,
"comment": null,
"user": 357
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEJ6_fit1_model2_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/SASDEJ6_fit1_model2.pdb",
"model_mw": 76.799,
"bead_radius": 3.0,
"log": null,
"symmetry": null,
"comment": null,
"user": 357
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/E2T1-BS69-483-507_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.4,
"p_value": 0.000312,
"fit_residual_plot": "E2T1-BS69-483-507_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEJ6_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/E2T1-BS69-483-507.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "SEC-SAXS was performed using the following parameters: Column type: S200 3.2/300 increase; Flow rate: 0.075 ml/min; Injection volume: 45 µl; Sample injection concentration: 9.0 mg/ml. The molar ratio of the injected sample components was 1:3 (EBNA2:BS69). The final complex contains four BS69 CC-MYND (2 dimers) with two EBNA2 Type1 (381-455) polypeptides.",
"experiment_description": "Synchrotron SAXS data from solutions of Epstein-Barr nuclear antigen 2 (EBNA2) bound to BS69 CC-MYND in 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The sample was measured using size exclusion chromatography SAXS (SEC-SAXS) at 25°C. 25 successive 3 second frames were collected through the SEC sample elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 69.4,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.01062,
"pddf_i0_error": null,
"guinier_i0": 0.0107,
"guinier_i0_error": 0.0001,
"pddf_rg": 4.65,
"pddf_rg_error": null,
"guinier_rg": 4.57,
"guinier_rg_error": 0.08,
"pddf_dmax": 13.83,
"pddf_dmax_error": null,
"porod_volume": 72.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 29,
"guinier_point_last": 84,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEJ6_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
