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": "SASDDR3",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/A",
"project": {
"title": "Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.",
"publication": {
"title": "Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.",
"author_list": "Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gkz856",
"pmid": "31586407",
"published_date": "2019 Oct 5"
},
"status": "released",
"submitted_date": "2018-02-27",
"released_date": "2019-10-06"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDR3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDR3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDR3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDR3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 2M",
"resolution": 0.172
},
"name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
"city": "Tsukuba",
"country": "Japan",
"beamline_name": "BL-10C",
"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": "Trm7: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase",
"short_name": "Trm7_yeast",
"sequence": "MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQVLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADFVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGYLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDKLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALELKRSGKLTRSVLEVLFQGPSHHHHHH",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "P38238",
"uniprot_range_first": 1,
"uniprot_range_last": 310,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQV\nLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADF\nVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGY\nLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDK\nLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALEL\nKRSGKLTRSV",
"mw": 36.494,
"total_mw": 36.494,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Trm734: Regulator of Ty1 transposition protein 10",
"short_name": "Trm734 (WDR6_yeast)",
"sequence": "MKDLSHYGPALCVKFYNDYVLAGYGPFIHVYDYHSATLINKCRLFHYNKVHGLSLSSEGKILAYGARSVTIVELEDVLKKESLVDFERINSDWITGATFSFDNLQIYLLTCYNKVLICDLNCEVLFRKSLGGERSILYSGIIKVFGPDKVYVNAGTVMGGVIIWDLFSETKIHNLLGHEGSIFYVNLSNNGRYVASCSDDRSIRLWDLETGKQLSVGWSHTARIWNLMFFDNDSKLISVSEDCTCRVWNIIESRENVAELSISNVYEVHLIKSIWGVDVKDDEMIAVTSGNDGRLKLIDLLQLKRHGDEETSFSLDDIAKQCGDIFEKNESIKGFQWFSFGVIAITSLGKILKYSDVTKQWKLLLTNEKFNSYPITNGIQTQNIAVFSNNKSDILLIKFSKDSADIIETEEFHLDELSKTNNCLVTEYDDDSFLLTLQSPNPREKFVCLEISLQNLKIKSKHCFNKPENFSSSCLTSFRNHILVGSRFSTLVIYNLLDESEEPFIIRRLSPGDTTTSIEFVEDKDNSAVFSVTNRDGYYVFIELTKNSLEEGPYRLSYKVLHSNKMMKGFLEGAFFNSKGEYITYGFKSSLFYLYNETNCYELASEVCGGSHRLWNLAKITDGHVLMYIKASRFHLRKIYNSIVPETLENGVHGREIRDISICPVSNTNTNDNFKDGHIFCTASEDTTIKLGYFNNRTGKVQNFWTQRKHVSGLQRCQFINHKLMISSSAREELFLWELNDKYNKRPYMTIRQALPVSTNNSDLRIMDFDVKFISQSGDFLLVTVYSDSTIKIWHYRENQNKFDLIMQGRYKTCCLFNVVFIALKEELLVVISPTDGHLVVYNITEYVPFSVDPISGDLVDHKLDATISNLPAPVAQLPVHQSGVKSLDYVANATRTSATILTGGDDNGLGLSNLKLDDSNKVTLKTSDFIAAAASSTITSGMLINGGKEVITTSVDQVIRAWEITAGKLSLVDKKRTTVADTGSLEIISNDEDADSEKTLLIGGVGLSIWKKLEVLFQGPSHHHHHH",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "Q08924",
"uniprot_range_first": 1,
"uniprot_range_last": 1013,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKDLSHYGPALCVKFYNDYVLAGYGPFIHVYDYHSATLINKCRLFHYNKVHGLSLSSEGK\nILAYGARSVTIVELEDVLKKESLVDFERINSDWITGATFSFDNLQIYLLTCYNKVLICDL\nNCEVLFRKSLGGERSILYSGIIKVFGPDKVYVNAGTVMGGVIIWDLFSETKIHNLLGHEG\nSIFYVNLSNNGRYVASCSDDRSIRLWDLETGKQLSVGWSHTARIWNLMFFDNDSKLISVS\nEDCTCRVWNIIESRENVAELSISNVYEVHLIKSIWGVDVKDDEMIAVTSGNDGRLKLIDL\nLQLKRHGDEETSFSLDDIAKQCGDIFEKNESIKGFQWFSFGVIAITSLGKILKYSDVTKQ\nWKLLLTNEKFNSYPITNGIQTQNIAVFSNNKSDILLIKFSKDSADIIETEEFHLDELSKT\nNNCLVTEYDDDSFLLTLQSPNPREKFVCLEISLQNLKIKSKHCFNKPENFSSSCLTSFRN\nHILVGSRFSTLVIYNLLDESEEPFIIRRLSPGDTTTSIEFVEDKDNSAVFSVTNRDGYYV\nFIELTKNSLEEGPYRLSYKVLHSNKMMKGFLEGAFFNSKGEYITYGFKSSLFYLYNETNC\nYELASEVCGGSHRLWNLAKITDGHVLMYIKASRFHLRKIYNSIVPETLENGVHGREIRDI\nSICPVSNTNTNDNFKDGHIFCTASEDTTIKLGYFNNRTGKVQNFWTQRKHVSGLQRCQFI\nNHKLMISSSAREELFLWELNDKYNKRPYMTIRQALPVSTNNSDLRIMDFDVKFISQSGDF\nLLVTVYSDSTIKIWHYRENQNKFDLIMQGRYKTCCLFNVVFIALKEELLVVISPTDGHLV\nVYNITEYVPFSVDPISGDLVDHKLDATISNLPAPVAQLPVHQSGVKSLDYVANATRTSAT\nILTGGDDNGLGLSNLKLDDSNKVTLKTSDFIAAAASSTITSGMLINGGKEVITTSVDQVI\nRAWEITAGKLSLVDKKRTTVADTGSLEIISNDEDADSEKTLLIGGVGLSIWKK",
"mw": 116.254,
"total_mw": 116.254,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES, 200 mM KCl, 5% v/v Glycerol, 10mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "KEK",
"address": "Tsukuba, Japan",
"full_name": "High Energy Accelerater Research Organization (KEK)",
"webpage": "https://www.kek.jp"
}
],
"contributor_name": "Kento",
"contributor_surname": "Yonezawa",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-12-16",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 20.0,
"number_of_frames": 40,
"wavelength": 0.1,
"sample_detector_distance": 2.05,
"concentration_min": 0.47,
"concentration_max": 3.1,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.063,
"s_max": 4.099,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDR3_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDR3_fit1_model1.pdb",
"model_mw": 141.44,
"bead_radius": 4.25,
"log": "https://www.sasbdb.org/media/log_files/zc_001_xuZHpHZ.log",
"symmetry": "P1",
"comment": null,
"user": 275
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDR3_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.917,
"p_value": 0.034809,
"fit_residual_plot": "SASDDR3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDR3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/zc_001_cMEHJMB.log",
"software_version": "ATSAS 2.7",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDR3_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDR3_fit2_model1.pdb",
"model_mw": 145.3,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/TRM04.log",
"symmetry": "P1",
"comment": null,
"user": 275
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDR3_fit2_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 2.18,
"p_value": 8e-06,
"fit_residual_plot": "SASDDR3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDR3_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/TRM04.log",
"software_version": "ATSAS 2.7",
"description": ""
}
],
"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 Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex in 50 mM HEPES-KOH, 200 mM, KCl, 5 % v/v glycerol, 10 mM β-mercaptoethanol, pH 8.0 were collected on the beam line BL-10C at the Phton Factory (PF; Tsukuba, Ibaraki, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2.05 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). 40 images of 20 second frames were collected at 20°C. The data were normalized to the intensity of the incident beam and circularly averaged; the scattering of the solvent-blank was subtracted. The extrapolated scattering profile at a concentration of zero was calculated PRIMUS QT of ATSAS.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 158.819,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 136.25,
"porod_mw_error": null,
"pddf_i0": 0.1921,
"pddf_i0_error": 0.0001,
"guinier_i0": 0.192981,
"guinier_i0_error": 0.0001,
"pddf_rg": 3.77,
"pddf_rg_error": 0.003,
"guinier_rg": 3.79,
"guinier_rg_error": 0.003,
"pddf_dmax": 12.99,
"pddf_dmax_error": null,
"porod_volume": 218.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 54,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDR3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
