查看完整 summary.json 原文
{
"code": "SASDF24",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.",
"publication": {
"title": "Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.",
"author_list": "Polykretis P, Luchinat E, Bonucci A, Giachetti A, Graewert MA, Svergun DI, Banci L",
"journal": "IUCrJ",
"doi": "10.1107/S205225251901073X",
"pmid": "31576227",
"published_date": "2019 Sep 1"
},
"status": "released",
"submitted_date": "2019-03-14",
"released_date": "2019-08-28"
},
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"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF24.dat",
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"experiment": {
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"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,
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},
"sample": {
"molecule": [
{
"long_name": "E3 ubiquitin-protein ligase XIAP",
"short_name": null,
"sequence": "MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\r\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\r\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\r\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\r\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\r\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\r\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\r\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\r\nCPMCYTVITFKQKIFMS",
"organism": "Homo sapiens",
"uniprot_code": "P98170",
"uniprot_range_first": 1,
"uniprot_range_last": 497,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\nCPMCYTVITFKQKIFMS",
"mw": 56.684,
"total_mw": 113.368,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "Xiap buffer",
"concentration_unit": null,
"comment": "20 mM Tris buffer, 0.5 mM TCEP,",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Full-length X-chromosome linked inhibitor of apoptosis protein (XIAP)",
"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": "Melissa ",
"contributor_surname": "Graewert",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-09-15",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 15,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 7.5,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.091,
"s_max": 5.064,
"total_exposure_time": null,
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},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF24_fit1_model1_img.png",
"software": "HADDOCK",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF24_fit1_model1.pdb",
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"bead_radius": null,
"log": null,
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"comment": null,
"user": 14
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/testGR1_372700_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.528,
"p_value": 5.3e-05,
"fit_residual_plot": "testGR1_372700_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF24_fit1.fit",
"fit_log": null,
"software_version": null,
"description": "A number of models were gennerated using HADDOCK (van Zundert, G. C. P. et al. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J. Mol. Biol. 428, 720–725 (2016).\r\nThese were screened against the SAXS data using Crysol. The model with the best fit is shown here.\r\nModel input: starting from the atomic structures of the individual domains: BIR1 (2POI.pdb), BIR2 (1I3O.pdb), BIR3 (5M6E.pdb), UBA (2KNA.pdb) and RING (5O6T.pdb)."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of X-chromosome linked inhibitor of apoptosis protein (XIAP) in Xiap buffer, pH 7.4 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Superdex 200 10/300 GL (GE healthcare Life Sciences); Flow rate: 0.5 mL/min; Sample injection concentration: 7.5 mg/mL; Injection volume: 100 μL. The data were collected through the SEC peak of the protein as a series of 15 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 115.0,
"experimental_mw_error": null,
"guinier_i0_mw": 0.0,
"guinier_i0_mw_error": null,
"porod_mw": 130.0,
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"pddf_i0": 16800.0,
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"guinier_i0": 16438.0,
"guinier_i0_error": 32.0,
"pddf_rg": 3.99,
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"guinier_rg": 3.86,
"guinier_rg_error": 0.06,
"pddf_dmax": 12.82,
"pddf_dmax_error": null,
"porod_volume": 207.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 34,
"guinier_point_last": 89,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF24_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}查看完整 manifest.json 原文
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"finished_at": "2026-08-11T14:12:24.962763+00:00",
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