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": "SASDFD4",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1.",
"publication": {
"title": "Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1.",
"author_list": "Manalastas-Cantos K, Kschonsak M, Haering CH, Svergun DI",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.RA119.008661",
"pmid": "31350339",
"published_date": "2019 Sep 13"
},
"status": "released",
"submitted_date": "2019-03-20",
"released_date": "2019-07-26"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFD4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFD4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFD4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"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": "Condensin complex subunit 3-like protein",
"short_name": "Ycg1",
"sequence": ">tr|G0SHK2|G0SHK2_CHATD Condensin complex subunit 3-like protein OS=Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) 24-1006\r\nPDNALRTQVTTVFREAQRTTASHRKLVVTLRKIQEACCYEPATGQKQSGAAAALSEFDED\r\nDFNTEFVRCALRILPVKKSEGVGEKTVRFVSLFLRHAIEKDNELLGDTQMDEDDADNSTM\r\nPETPSTRLTSHLMETILPMLMAKDKFVRYRAAQLLAHIVNSLDAIDDDLYQKLRAGLLRR\r\nIHDKEPMVRAQAVLGLGRLAGNALDEEPGAGDSDLDGDDDGPGGASGVSLMDKLMDVMKN\r\nDPSADVRRTLLVNLPITPKTLPSLLERARDQDPATRRAVYSRLLPALGDFRHLSLSMREK\r\nLLRWGLRDRDENVRKAAARLFRERWIEDCAGTPRPEPGQPIELSPPNMDALLELLERIDV\r\nVNSGGENGIALEAMRGFWEGRPDYRDAMVFDDHFFETLSAESVFALRTFNDFCRNEAGGK\r\nYEALIEEKLPEVTKLAFYLERYIKVLIDAIKRAEEQGEEEEEDTAEQEFIVEQLLHIALT\r\nLDYADEVGRRKMFALLRQTLSIPELPEECTKLTVMVLRDLCAPDAAGEKEFTSVVLEAVA\r\nDVHDTIVDEDDDDANVPAEDDESFVSARSEVSRESTPAPGGGEGGGSNSRKRGRSPTPKM\r\nTEEEAAAKAIREIMINMKCLHIVQCMLQNVQGQLQSNDNLISMLNNLVVPAVRSHEAPVR\r\nERGLVCLGLCALLDRSLAEENLTLFIHFFAKGHTALQITALHILTDILVVHGAQLLSANP\r\nTLLKVYVKALRSGAKHPELQAVAVVAASKLLLGRVVSDRDVAAELLKTLVVAYFEPASAG\r\nNQSVRQALNYFLPVFCYSRAENQDLMRRVALDALHTLYNVREGFDDDDADIDDEMVSLAT\r\nIGACLVDWTDPRKVYTPDAGGLQAEKHVNADVHLDFAKAILERLEGNVPREEKKVLASLL\r\nSKLYISPASSPDKTRETYRVVSAAVDTNLLPDTTSRNALYKIHVSLGKIVNALDGAVPSV\r\nETASVAGSTGTGIGTTTTAATGR",
"organism": "Chaetomium thermophilum",
"uniprot_code": "G0SHK2",
"uniprot_range_first": 24,
"uniprot_range_last": 1006,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPPRTRSTRSSRSSSAIDIPEETPDNALRTQVTTVFREAQRTTASHRKLVVTLRKIQEAC\nCYEPATGQKQSGAAAALSEFDEDDFNTEFVRCALRILPVKKSEGVGEKTVRFVSLFLRHA\nIEKDNELLGDTQMDEDDADNSTMPETPSTRLTSHLMETILPMLMAKDKFVRYRAAQLLAH\nIVNSLDAIDDDLYQKLRAGLLRRIHDKEPMVRAQAVLGLGRLAGNALDEEPGAGDSDLDG\nDDDGPGGASGVSLMDKLMDVMKNDPSADVRRTLLVNLPITPKTLPSLLERARDQDPATRR\nAVYSRLLPALGDFRHLSLSMREKLLRWGLRDRDENVRKAAARLFRERWIEDCAGTPRPEP\nGQPIELSPPNMDALLELLERIDVVNSGGENGIALEAMRGFWEGRPDYRDAMVFDDHFFET\nLSAESVFALRTFNDFCRNEAGGKYEALIEEKLPEVTKLAFYLERYIKVLIDAIKRAEEQG\nEEEEEDTAEQEFIVEQLLHIALTLDYADEVGRRKMFALLRQTLSIPELPEECTKLTVMVL\nRDLCAPDAAGEKEFTSVVLEAVADVHDTIVDEDDDDANVPAEDDESFVSARSEVSRESTP\nAPGGGEGGGSNSRKRGRSPTPKMTEEEAAAKAIREIMINMKCLHIVQCMLQNVQGQLQSN\nDNLISMLNNLVVPAVRSHEAPVRERGLVCLGLCALLDRSLAEENLTLFIHFFAKGHTALQ\nITALHILTDILVVHGAQLLSANPTLLKVYVKALRSGAKHPELQAVAVVAASKLLLGRVVS\nDRDVAAELLKTLVVAYFEPASAGNQSVRQALNYFLPVFCYSRAENQDLMRRVALDALHTL\nYNVREGFDDDDADIDDEMVSLATIGACLVDWTDPRKVYTPDAGGLQAEKHVNADVHLDFA\nKAILERLEGNVPREEKKVLASLLSKLYISPASSPDKTRETYRVVSAAVDTNLLPDTTSRN\nALYKIHVSLGKIVNALDGAVPSVETASVAGSTGTGIGTTTTAATGRRVTRGSVSAGSGTG\nAGRRSISRASSVSTNADRPASASAAVPGSKAASTIEEEEEKEQEEEEEEEEKEEKEEEEE\nEEEEENVDEETQLAMQLQADTTAAQSREGSVQIKREEDDSESEASDATVVRGSVGTGRRV\nKQEEDDDF",
"mw": 108.325,
"total_mw": 108.325,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Condensin complex subunit 2",
"short_name": "Brn1",
"sequence": ">tr|G0SBJ6|G0SBJ6_CHATD Condensin complex subunit 2 OS=Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) 515-634\r\nKIHEDILSYFDQALQKNWTSAEHWRIRKIKDVNKPNEPTRQRKEKQPFEIDFVSPLDKAL\r\nAEIIYTKASSNATISMPKKDWKSKTKNLLPDDKHFSSKQLLSLFLKPKARMGRRRVLKTS",
"organism": "Chaetomium thermophilum",
"uniprot_code": "G0SBJ6",
"uniprot_range_first": 515,
"uniprot_range_last": 634,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPRVAPHRRSGSRVGSGSFLESPFKSPAKLPLADDAIEKAERAQGRKAAHEAQINQIRSA\nATSTPRKSSGAFNPDLDHGASPNSTPRTPHRRRSAVRETILLDDEEVVVGGRAVTPMKRV\nPILANFEEWMKMATDNKINAANSWNFALIDYFHDMSLLKEGDSVNFQKASCTLDGCVKIY\nTSRVDSVATETGKLLSGLADSRDSKKKDREDGGEDDDEEEEEVDEDGTVRKKPKKKTQRS\nSEATLAPSFASLQLKKLELEFAVDPFFKKASADFDEGGAKGLLLNHLMIDSQGRIVFDSS\nDDAEDVAEASAKPSREADDERPDSEDADADGDISMTDRDASAPGQVETQPEEEDEDVEID\nVAALGAKYFPDLSILDSLDVCPSLKTFDLGDPSGSLYIPFLKVPDDWRHDQEKEKTPGLG\nSLGNKSAMFIDDENPDGFDDDDGLGTFDMGADVGFGEGGEAWAKEAALEPHAMRVYDAGL\nGDGTEGDGEGDGADLMDAGTGEYVVAMSQPRSAEKIHEDILSYFDQALQKNWTSAEHWRI\nRKIKDVNKPNEPTRQRKEKQPFEIDFVSPLDKALAEIIYTKASSNATISMPKKDWKSKTK\nNLLPDDKHFSSKQLLSLFLKPKARMGRRRVLKTSRIGNIDSERHDDLPEGEVDEAFWATQ\nKAPLANGNDRPGRHPDDDDEPLPQGDYDANFFADDGLPFAGGMDDDDDMDRFSDAREHFS\nPEPGAGGPGMNSTAGLQDLATGIMGQNPGDGAFGTNLVTQGRRVRPEYVQYARVAKKVDV\nRRLKEEIWKGMGFDELTSSNSNDTSQLQTPARQAEEQRSPESADGPNGKDKDPTLRFTDV\nMNSLQRVYPKQVMDDISTSYCFICLLHLANEKGLVIEKTDTLDELYIRKDWSAVVGDE",
"mw": 17.0,
"total_mw": 17.0,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM Tris, 300 mM NaCl, 1mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Condensin complex subunit 3-like protein,Ycg1, bound to condensin complex subunit 2, Brn1 (Ycg1-Brn1)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Karen",
"contributor_surname": "Manalastas-Cantos",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-10-20",
"storage_temperature": 13.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 4.0,
"concentration_min": 0.5,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.047,
"s_max": 2.511,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD4_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.8.3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD4_fit1_model1.pdb",
"model_mw": 153.0,
"bead_radius": 1.7,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 425
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ycg1-kle-5_su5qzO1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.684,
"p_value": 0.003314,
"fit_residual_plot": "ycg1-kle-5_su5qzO1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD4_fit1.fir",
"fit_log": null,
"software_version": "2.8.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD4_fit2_model1_img.png",
"software": "SREFLEX",
"pdb_link": [
{
"pdb_code": "5oqq",
"ext_code": "5OQQ",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD4_fit2_model1.pdb",
"model_mw": 106.0,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/log_TC1Jeri.txt",
"symmetry": "P1",
"comment": null,
"user": 425
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/rc01_6iVq9ds_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.935,
"p_value": 0.0,
"fit_residual_plot": "rc01_6iVq9ds_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD4_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/rc01_KqVj408.log",
"software_version": "2.8.3",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "2.8.3",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the Ycg1-Brn1 complex in 25 mM Tris 300 mM NaCl 1mM DTT, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 5 mg/ml were measured at 10°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 138.0,
"experimental_mw_error": null,
"guinier_i0_mw": 122.0,
"guinier_i0_mw_error": null,
"porod_mw": 144.0,
"porod_mw_error": null,
"pddf_i0": 9503.0,
"pddf_i0_error": null,
"guinier_i0": 9640.0,
"guinier_i0_error": 55.0,
"pddf_rg": 4.186,
"pddf_rg_error": null,
"guinier_rg": 4.25,
"guinier_rg_error": 0.1,
"pddf_dmax": 13.73,
"pddf_dmax_error": null,
"porod_volume": 230.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 24,
"guinier_point_last": 122,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFD4_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
