查看完整 summary.json 原文
{
"code": "SASDBR9",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/nm",
"project": {
"title": "Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System.",
"publication": {
"title": "Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System.",
"author_list": "Bunney TD, Inglis AJ, Sanfelice D, Farrell B, Kerr CJ, Thompson GS, Masson GR, Thiyagarajan N, Svergun DI, Williams RL, Breeze AL, Katan M",
"journal": "Structure",
"doi": "10.1016/j.str.2018.01.016",
"pmid": "29478821",
"published_date": "2018 Mar 6"
},
"status": "released",
"submitted_date": "2017-01-18",
"released_date": "2018-03-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBR9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBR9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBR9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBR9.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": "Fibroblast growth factor receptor 3",
"short_name": "FGFR3",
"sequence": "SELELPADPKWELSRARLTLGKPLGEGAFGQVVMAEAIGIDKDRAAKPVTVA\r\nVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNFINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTSKPPE\r\nEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEAL\r\nFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVE\r\nDLDRVLTVTSTDEYLDLSAPFE",
"organism": "Homo sapiens",
"uniprot_code": "P22607",
"uniprot_range_first": 455,
"uniprot_range_last": 768,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGAPACALALCVAVAIVAGASSESLGTEQRVVGRAAEVPGPEPGQQEQLVFGSGDAVELS\nCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSCRQRLTQRVLCH\nFSVRVTDAPSSGDDEDGEDEAEDTGVDTGAPYWTRPERMDKKLLAVPAANTVRFRCPAAG\nNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQT\nYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGP\nDGTPYVTVLKTAGANTTDKELEVLSLHNVTFEDAGEYTCLAGNSIGFSHHSAWLVVLPAE\nEELVEADEAGSVYAGILSYGVGFFLFILVVAAVTLCRLRSPPKKGLGSPTVHKISRFPLK\nRQVSLESNASMSSNTPLVRIARLSSGEGPTLANVSELELPADPKWELSRARLTLGKPLGE\nGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIIN\nLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCAYQ\nVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKW\nMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCT\nHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSAPFEQYSPGGQDTPSS\nSSSGDDSVFAHDLLPPAPPSSGGSRT",
"mw": 35.478,
"total_mw": 35.478,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM Tris.Cl, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Human fibroblast growth factor receptor 3, from SEC-SAXS",
"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": "Chris",
"contributor_surname": "Kerr",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-07-10",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 3600,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
"concentration_min": 0.0,
"concentration_max": 2.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.025,
"s_max": 5.031,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR9_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "4k33",
"ext_code": "4K33",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "ATSAS2.7.2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR9_fit1_model1.pdb",
"model_mw": 79.77,
"bead_radius": 3.5,
"log": "https://www.sasbdb.org/media/log_files/CDCFGF_cLVEuwL.log",
"symmetry": "P1",
"comment": "",
"user": 55
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBR9_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 3.1,
"p_value": 0.0,
"fit_residual_plot": "SASDBR9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBR9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CDCFGF_cNap9M5.log",
"software_version": "ATSAS2.7.2",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR9_fit2_model1_img.png",
"software": "MONSA",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "ATSAS2.7.2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR9_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 3.0,
"log": "https://www.sasbdb.org/media/log_files/CDCFGF_P1u6l2X.log",
"symmetry": "P1",
"comment": "",
"user": 55
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBR9_fit2_fit_img.png",
"software": "MONSA",
"chi_square_value": 1.2,
"p_value": 0.0,
"fit_residual_plot": "SASDBR9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBR9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CDCFGF_Rt1zSo7.log",
"software_version": "ATSAS2.7.2",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM5 - trunk r8992",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Human fibroblast growth factor receptor 3 in 25 mM Tris-HCl, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP, pH 8, were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the P12 beam line at the PETRA III storage ring (Hamburg, Germany) equipped with a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). The scattering pattern was extracted from the SEC-SAXS intensity data (weighted for the estimated errors) using the non-negative matrix factorization (NMF) algorithm as implemented in the scikit-learn package. The NMF fit was done with four components (one of which corresponds to the buffer), and the component with Guinier radius closest to that expected for FGFR3 was selected for further analysis.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 29.3,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 29.3,
"porod_mw_error": null,
"pddf_i0": 183.1,
"pddf_i0_error": 0.3181,
"guinier_i0": 183.31,
"guinier_i0_error": 0.38,
"pddf_rg": 2.363,
"pddf_rg_error": 0.007,
"guinier_rg": 2.35,
"guinier_rg_error": 0.27,
"pddf_dmax": 8.3,
"pddf_dmax_error": 3.0,
"porod_volume": 59.45,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 78,
"guinier_point_last": 192,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBR9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
