查看完整 summary.json 原文
{
"code": "SASDFA6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.",
"publication": {
"title": "The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.",
"author_list": "Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T",
"journal": "Mol Microbiol",
"doi": "10.1111/mmi.14396",
"pmid": "31556164",
"published_date": "2019 Sep 25"
},
"status": "released",
"submitted_date": "2019-05-08",
"released_date": "2019-09-24"
},
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"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Australian Synchrotron",
"city": "Melbourne",
"country": "Australia",
"beamline_name": "SAXS/WAXS",
"beam_geometry": "Point",
"type_of_source": "X-ray synchrotron",
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},
"sample": {
"molecule": [
{
"long_name": "Flagella binding tail protein",
"short_name": "YSD1_29",
"sequence": "IRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPAIARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFDVRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAEEFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPWTLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGETPDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTTYTIRVYNQEGTLVRTESGINGTTWNWPYATAAADMNVEASLFDPVLATLRLTSVRNGRESWEYYEMKVSVYKKPPQFVYDASLMQFAAQPYNATIDPNPPTPPMDGPYVSALMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQTSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYTSAGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAINGRTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSKLYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRVSQSTTARDHFAVGINPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLERWGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNPPGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEPPVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPELEHHHHHH",
"organism": "Salmonella virus Chi",
"uniprot_code": "M9NVD3",
"uniprot_range_first": 373,
"uniprot_range_last": 1296,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGSKSKKVTVGYKYYMGLFMGLFRGPVNEITEIRVGDRTAWTGSITGNTTIQINKESLFG\nGTKAEGGIDGPLEVYMGAPTQTVSQKLKNMLGGRQPEFRGVVTAYFDGLICAMNPYPKQW\nKFKARRSTAGWTGGVWYPEKCLVKMQGYDGQGNQHEIHAMNPAHILYECQSNYEWGRGLS\nRTLIDDTTFRLAADTLFNENFGLCIRWNRQDTLESFMQLILDHIGGAMYVSKVTGKLSLR\nLIRKDYDFDTLPIFDTDSGLLSIQEATNASPANLVNEVVVTYHNPVMDEDQQVRSHNLAQ\nIQNQGCLNSNTIEYLGIPTGKLAMQVAQRDLRAASTNVRRFTVICDRRAWNVQPGDVLKV\nRDPKQRGLTEVVIRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPA\nIARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFD\nVRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAE\nEFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPW\nTLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGET\nPDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTSYTIRVYNQEGTLVRTESGINGTTWN\nWPYATAAADMNVEASLFDPVLATLRLTSARNGRESWEYYEMKVSVYKKPPQFVYDASLMQ\nFAAQPYNATSDPNPPTPPMDGPYVSSLMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQ\nTSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYT\nSSGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAING\nRTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSK\nLYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRV\nSQSTTARDHFAVGITPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLER\nWGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNP\nPGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEP\nPVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPE",
"mw": 102.637,
"total_mw": 102.637,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
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"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.8,
"deuteration": null
},
"purity_method": null,
"name": "Proteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Melbourne, Australia",
"full_name": "Monash University",
"webpage": "http://www.monash.edu/"
}
],
"contributor_name": "Grinter",
"contributor_surname": "Grinter",
"orcid": "https://orcid.org/0000-0002-8195-5348"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-04-04",
"storage_temperature": 4.0,
"cell_temperature": 23.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.10322,
"sample_detector_distance": 1.426,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 100.0,
"flow_rate": 0.4,
"s_min": 0.057,
"s_max": 3.169,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
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{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFA6_fit1_model1_img.png",
"software": "DAMMIF",
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"model_title": null,
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"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFA6_fit1_model1.pdb",
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"bead_radius": 5.0,
"log": null,
"symmetry": null,
"comment": null,
"user": 322
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/YSD29_800_4SccVAl_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.504,
"p_value": 2e-05,
"fit_residual_plot": "YSD29_800_4SccVAl_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFA6_fit1.fir",
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"description": ""
}
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"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
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"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Proteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296) in 20 mM Tris, 150 mM NaCl, 0.03 % NaN3, 5.0 % glycerol, pH 7.8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.4 m and at a wavelength of λ = 0.10322 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed. The SEC parameters were as follows: A 100 μl sample at 10 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 23°C. 10 successive 1 second frames were collected through the SEC-elution peak. 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",
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"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 97.0,
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"pddf_i0": 0.279,
"pddf_i0_error": null,
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"porod_volume": 155.0,
"porod_volume_error": null,
"estimated_volume": null,
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"guinier_point_first": 3,
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"pddf_point_first": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFA6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-07-03T15:26:52.401701+02:00",
"bragg_peak": []
}查看完整 manifest.json 原文
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