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": "SASDG44",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.",
"publication": {
"title": "Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.",
"author_list": "Vassal-Stermann E, Hutin S, Fender P, Burmeister WP",
"journal": "Acta Crystallogr F Struct Biol Commun",
"doi": "10.1107/S2053230X19015784",
"pmid": "31797817",
"published_date": "2019 Dec 1"
},
"status": "released",
"submitted_date": "2019-08-13",
"released_date": "2019-12-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG44.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG44.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG44_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG44.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"beam_geometry": "",
"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": "Human adenovirus serotype 3 fibre knob",
"short_name": "HAd3K",
"sequence": "HHHHHHSQDPANSIALKNNTLWTGPKPEANCIIEYGKQNPDSKLTLILVKNGGIVNGYVTLMGASDYVNTLFKNKNVSINVELYFDATGHILPDSSSLKTDLELKYKQTADFSARGFMPSTTAYPFVLPNAGTHNENYIFGQCYYKASDGALFPLEVTVMLNKRLPDSRTSYVMTFLWSLNAGLAPETTQATLITSPFTFSYIREDD",
"organism": "Human adenovirus serotype 3",
"uniprot_code": "P04501",
"uniprot_range_first": 130,
"uniprot_range_last": 318,
"oligomerization": "trimer",
"molecular_type": "protein",
"uniprot_sequence": "MAKRARLSTSFNPVYPYEDESSSQHPFINPGFISPDGFTQSPNGVLSLKCVNPLTTASGS\nLQLKVGSGLTVDTTDGSLEENIKVNTPLTKSNHSINLPIGNGLQIEQNKLCSKLGNGLTF\nDSSNSIALKNNTLWTGPKPEANCIIEYGKQNPDSKLTLILVKNGGIVNGYVTLMGASDYV\nNTLFKNKNVSINVELYFDATGHILPDSSSLKTDLELKYKQTADFSARGFMPSTTAYPFVL\nPNAGTHNENYIFGQCYYKASDGALFPLEVTVMLNKRLPDSRTSYVMTFLWSLNAGLAPET\nTQATLITSPFTFSYIREDD",
"mw": 23.072,
"total_mw": 69.216,
"number_molecules": 3,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Human desmoglein 2 extracellular domain 2 and 3",
"short_name": "EC2-EC3",
"sequence": "QGAMEVLDINDNEPVFTQDVFVGSVEELSAAHTLVMKINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVEARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADEIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAFHKSIRSKYKPTPIPIKVKVKNVKEGI",
"organism": "Homo sapiens",
"uniprot_code": "Q14126",
"uniprot_range_first": 157,
"uniprot_range_last": 380,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MARSPGRAYALLLLLICFNVGSGLHLQVLSTRNENKLLPKHPHLVRQKRAWITAPVALRE\nGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDRE\nETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQDVFVGSVEELSAAHTLVMK\nINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVE\nARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADE\nIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAF\nHKSIRSKYKPTPIPIKVKVKNVKEGIHFKSSVISIYVSESMDRSSKGQIIGNFQAFDEDT\nGLPAHARYVKLEDRDNWISVDSVTSEIKLAKLPDFESRYVQNGTYTVKIVAISEDYPRKT\nITGTVLINVEDINDNCPTLIEPVQTICHDAEYVNVTAEDLDGHPNSGPFSFSVIDKPPGM\nAEKWKIARQESTSVLLQQSEKKLGRSEIQFLISDNQGFSCPEKQVLTLTVCECLHGSGCR\nEAQHDSYVGLGPAAIALMILAFLLLLLVPLLLLMCHCGKGAKGFTPIPGTIEMLHPWNNE\nGAPPEDKVVPSFLPVDQGGSLVGRNGVGGMAKEATMKGSSSASIVKGQHEMSEMDGRWEE\nHRSLLSGRATQFTGATGAIMTTETTKTARATGASRDMAGAQAAAVALNEEFLRNYFTDKA\nASYTEEDENHTAKDCLLVYSQEETESLNASIGCCSFIEGELDDRFLDDLGLKFKTLAEVC\nLGQKIDINKEIEQRQKPATETSMNTASHSLCEQTMVNSENTYSSGSSFPVPKSLQEANAE\nKVTQEIVTERSVSSRQAQKVATPLPDPMASRNVIATETSYVTGSTMPPTTVILGPSQPQS\nLIVTERVYAPASTLVDQPYANEGTVVVTERVIQPHGGGSNPLEGTQHLQDVPYVMVRERE\nSFLAPSSGVQPTLAMPNIAVGQNVTVTERVLAPASTLQSSYQIPTENSMTARNTTVSGAG\nVPGPLPDFGLEESGHSNSTITTSSTRVTKHSTVQHSYS",
"mw": 27.339,
"total_mw": 54.678,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl, 150 mM NaCl, 3 mM CaCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "IBS",
"address": "Grenoble, France",
"full_name": "Institut de Biologie Structurale",
"webpage": ""
}
],
"contributor_name": "Wim",
"contributor_surname": "Burmeister",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-01-26",
"storage_temperature": 293.0,
"cell_temperature": 293.0,
"exposure_time": 1.0,
"number_of_frames": 2000,
"wavelength": 0.099,
"sample_detector_distance": 2.864,
"concentration_min": null,
"concentration_max": 2.4,
"sample_volume": 100.0,
"flow_rate": 0.1,
"s_min": 0.141,
"s_max": 2.005,
"total_exposure_time": null,
"seccolumn": 14
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit1_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6sit",
"ext_code": "6SIT",
"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/SASDG44_fit1_model1.pdb",
"model_mw": 90.53,
"bead_radius": null,
"log": null,
"symmetry": "3-fold",
"comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.",
"user": 226
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.795,
"p_value": 0.0,
"fit_residual_plot": "SASDG44_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex3-100.log",
"software_version": "7.1",
"description": "3:1 complex present in 40 % of the particles"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit2_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6sit",
"ext_code": "6SIT",
"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/SASDG44_fit2_model1.pdb",
"model_mw": 117.3,
"bead_radius": null,
"log": null,
"symmetry": "3-fold",
"comment": "3:2 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.",
"user": 226
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.514,
"p_value": 0.0,
"fit_residual_plot": "SASDG44_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex3-200.log",
"software_version": "7.1",
"description": "Fit with the £:2 complex structure, present in 40 % of the particles."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit3_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6sit",
"ext_code": "6SIT",
"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/SASDG44_fit3_model1.pdb",
"model_mw": 90.53,
"bead_radius": null,
"log": null,
"symmetry": "3-fold",
"comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.",
"user": 226
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit3_model2_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6sit",
"ext_code": "6SIT",
"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/SASDG44_fit3_model2.pdb",
"model_mw": 117.3,
"bead_radius": null,
"log": null,
"symmetry": "3-fold",
"comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.",
"user": 226
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit3_fixed_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 0.4,
"p_value": 1e-06,
"fit_residual_plot": "SASDG44_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_MG0kL7h.log",
"software_version": "7.1",
"description": "Combination of 40 % 3:1 and 60 % 3:2 complexes (by number)."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "Three different stoichiometries are possible for the Had3K: human desmoglein 2 EC2-EC3 complex : 3:1, 3:2 and 3:3. The SAXS experiment is used in order to determine the possible stoichiometries in solution.",
"experiment_description": "Synchrotron SAXS data from solutions of adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2 in 20 mM Tris-HCl, 150 mM NaCl, 3 mM CaCl2, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 2.4 mg/ml was injected at a 0.10 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 293°C. 2000 successive 1 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 119.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 114.0,
"porod_mw_error": null,
"pddf_i0": 258.3,
"pddf_i0_error": null,
"guinier_i0": 255.03,
"guinier_i0_error": 0.61,
"pddf_rg": 3.5,
"pddf_rg_error": null,
"guinier_rg": 3.42,
"guinier_rg_error": 0.1,
"pddf_dmax": 11.17,
"pddf_dmax_error": null,
"porod_volume": 188.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 35,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDG44_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
