查看完整 summary.json 原文
{
"code": "SASDCN5",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/nm",
"project": {
"title": "The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.",
"publication": {
"title": "The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.",
"author_list": "Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F",
"journal": "Nat Commun",
"doi": "10.1038/s41467-017-01542-z",
"pmid": "29129932",
"published_date": "2017 Nov 13"
},
"status": "released",
"submitted_date": "2017-06-27",
"released_date": "2017-11-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCN5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCN5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCN5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCN5.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": "DNA polymerase E9",
"short_name": "E9",
"sequence": "GAMDPDVRCINWFESHGENRFLYLKSRCRNGETVFIRFPHYFYYVVTDEIYQSLSPPPFNARPLGKMRTIDIDETISYNL\r\nDIKDRKCSVADMWLIEEPKKRSIQNATMDEFLNISWFYISNGISPDGCYSLDEQYLTKINNGCYHCDDPRNCFAKKIPRF\r\nDIPRSYLFLDIECHFDKKFPSVFINPISHTSYCYIDLSGKRLLFTLINEEMLTEQEIQEAVDRGCLRIQSLMEMDYEREL\r\nVLCSEIVLLRIAKQLLELTFDYVVTFNGHNFDLRYITNRLELLTGEKIIFRSPDKKEAVHLCIYERNQSSHKGVGGMANT\r\nTFHVNNNNGTIFFDLYSFIQKSEKLDSYKLDSISKNAFSCMGKVLNRGVREMTFIGDDTTDAKGKAAAFAKVLTTGNYVT\r\nVDEDIICKVIRKDIWENGFKVVLLCPTLPNDTYKLSFGKDDVDLAQMYKDYNLNIALDMARYCIHDACLCQYLWEYYGVE\r\nTKTDAGASTYVLPQSMVFEYRASTVIKGPLLKLLLETKTILVRSETKQKFPYEGGKVFAPKQKMFSNNVLIFDYNSLYPN\r\nVCIFGNLSPETLVGVVVSTNRLEEEINNQLLLQKYPPPRYITVHCEPRLPNLISEIAIFDRSIEGTIPRLLRTFLAERAR\r\nYKKMLKQATSSTEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLESVLNGAELSNGMLRFAN\r\nPLSNPFYMDDRDINPIVKTSLPIDYRFRFRSVYGDTDSVFTEIDSQDVDKSIEIAKELERLINNRVLFNNFKIEFEAVYK\r\nNLIMQSKKKYTTMKYSASSNSKSVPERINKGTSETRRDVSKFHKNMIKTYKTRLSEMLSEGRMNSNQVCIDILRSLETDL\r\nRSEFDSRSSPLELFMLSRMHHSNYKSADNPNMYLVTEYNKNNPETIELGERYYFAYICPANVPWTKKLVNIKTYETIIDR\r\nSFKLGSDQRIFYEVYFKRLTSEIVNLLDNKVLCISFFERMFGSKPTFYEA",
"organism": "Vaccinia virus",
"uniprot_code": "P20509",
"uniprot_range_first": 1,
"uniprot_range_last": 1006,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDVRCINWFESHGENRFLYLKSRCRNGETVFIRFPHYFYYVVTDEIYQSLSPPPFNARPL\nGKMRTIDIDETISYNLDIKDRKCSVADMWLIEEPKKRSIQNATMDEFLNISWFYISNGIS\nPDGCYSLDEQYLTKINNGCYHCDDPRNCFAKKIPRFDIPRSYLFLDIECHFDKKFPSVFI\nNPISHTSYCYIDLSGKRLLFTLINEEMLTEQEIQEAVDRGCLRIQSLMEMDYERELVLCS\nEIVLLRIAKQLLELTFDYVVTFNGHNFDLRYITNRLELLTGEKIIFRSPDKKEAVHLCIY\nERNQSSHKGVGGMANTTFHVNNNNGTIFFDLYSFIQKSEKLDSYKLDSISKNAFSCMGKV\nLNRGVREMTFIGDDTTDAKGKAAAFAKVLTTGNYVTVDEDIICKVIRKDIWENGFKVVLL\nCPTLPNDTYKLSFGKDDVDLAQMYKDYNLNIALDMARYCIHDACLCQYLWEYYGVETKTD\nAGASTYVLPQSMVFEYRASTVIKGPLLKLLLETKTILVRSETKQKFPYEGGKVFAPKQKM\nFSNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVSTNRLEEEINNQLLLQKYPPPRYITVH\nCEPRLPNLISEIAIFDRSIEGTIPRLLRTFLAERARYKKMLKQATSSTEKAIYDSMQYTY\nKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLESVLNGAELSNGMLRFANPLSN\nPFYMDDRDINPIVKTSLPIDYRFRFRSVYGDTDSVFTEIDSQDVDKSIEIAKELERLINN\nRVLFNNFKIEFEAVYKNLIMQSKKKYTTMKYSASSNSKSVPERINKGTSETRRDVSKFHK\nNMIKTYKTRLSEMLSEGRMNSNQVCIDILRSLETDLRSEFDSRSSPLELFMLSRMHHSNY\nKSADNPNMYLVTEYNKNNPETIELGERYYFAYICPANVPWTKKLVNIKTYETIIDRSFKL\nGSDQRIFYEVYFKRLTSEIVNLLDNKVLCISFFERMFGSKPTFYEA",
"mw": 117.242,
"total_mw": 117.242,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris HCl, 100 mM NaCl, 4 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Vaccinia virus DNA polymerase",
"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": "2014-11-27",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 900,
"wavelength": 0.0992,
"sample_detector_distance": 2.864,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.079,
"s_max": 2.638,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCN5_fit1_model1_img.png",
"software": "PyMOL",
"pdb_link": [
{
"pdb_code": "5n2e",
"ext_code": "5N2E",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "1.6",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCN5_fit1_model1.pdb",
"model_mw": 116.1,
"bead_radius": 1.7,
"log": "https://www.sasbdb.org/media/log_files/e9.log",
"symmetry": "none",
"comment": "Calculated scattering curve of protein",
"user": 226
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCN5_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.569,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCN5_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/e9.log",
"software_version": "2.8.3",
"description": null
}
],
"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 Vaccinia virus DNA polymerase in 20 mM Tris HCl, 100 mM NaCl, 4 mM DTT, pH 7 using size exclusion chromatography coupled SAXS (SEC-SAXS) 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 = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data were collected at at 20°C during the course of elution (900 successive 1 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the resulting subtracted curves were scaled and averaged.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 117.0,
"experimental_mw_error": null,
"guinier_i0_mw": 0.0,
"guinier_i0_mw_error": null,
"porod_mw": 117.0,
"porod_mw_error": null,
"pddf_i0": 27.0,
"pddf_i0_error": 0.09,
"guinier_i0": 19.97,
"guinier_i0_error": 0.05,
"pddf_rg": 3.55,
"pddf_rg_error": 0.01,
"guinier_rg": 3.9,
"guinier_rg_error": 0.2,
"pddf_dmax": 12.0,
"pddf_dmax_error": null,
"porod_volume": 202.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 45,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCN5_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}查看完整 manifest.json 原文
{
"code": "SASDCN5",
"status": "success",
"started_at": "2026-08-11T14:51:36.414353+00:00",
"finished_at": "2026-08-11T14:51:45.422066+00:00",
"source_last_modified": "2019-12-06T13:07:15.624532+01:00",
"files": [
{
"status": "downloaded",
"url": "https://www.sasbdb.org/rest-api/entry/summary/SASDCN5/",
"path": "/data/saxsdb/sasbdb/entries/n5/sasdcn5/source/summary.json",
"size": 9292,
"sha256": "3322c372f1f7d6d7e780914e244a2962bb0041ff43a9ab3084b2c2cd26729001"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/intensities_files/SASDCN5.dat",
"path": "/data/saxsdb/sasbdb/entries/n5/sasdcn5/source/SASDCN5.dat",
"size": 24404,
"sha256": "4bad9de58338b790f0198bdf9579ed6c4c0f40b2bcacd3ef389793eccf360d8a",
"role": "curve"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/p_of_R_files/SASDCN5.out",
"path": "/data/saxsdb/sasbdb/entries/n5/sasdcn5/source/SASDCN5.out",
"size": 45755,
"sha256": "c1431772dbea1def0093d3d603f60fbbd9336cee5dc8f1aaedd18a5f651f3462",
"role": "pddf"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCN5.sascif",
"path": "/data/saxsdb/sasbdb/entries/n5/sasdcn5/source/SASDCN5.sascif",
"size": 943055,
"sha256": "104d847aa1789c2899a89dc18700e91d3506f350667f7b58836abc7d6c3ba01d",
"role": "sascif"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/zip_directories/SASDCN5.zip",
"path": "/data/saxsdb/sasbdb/entries/n5/sasdcn5/source/SASDCN5.zip",
"size": 193102,
"sha256": "a5baf5144d77a48b4161f507c804e3d9b133f6a8d204b0c41340cc8611b33b6b",
"role": "full_entry_zip",
"zip_member_count": 4,
"zip_validation": "central_directory_readable"
}
]
}
