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{
"code": "SASDBN8",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
"publication": {
"title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
"author_list": "Shah N, Beckham SA, Wilce JA, Wilce MCJ",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gkx1307",
"pmid": "29346611",
"published_date": "2018 Apr 6"
},
"status": "released",
"submitted_date": "2016-12-11",
"released_date": "2018-01-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBN8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBN8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBN8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBN8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBN8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBN8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBN8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"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",
"point_source": true,
"line_collimation": null,
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"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Probable ATP-dependent RNA helicase DDX58 (without CARDs)",
"short_name": "DC-RIG-I",
"sequence": "MHHHHHHAAASPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK",
"organism": "Homo sapiens",
"uniprot_code": "O95786",
"uniprot_range_first": 239,
"uniprot_range_last": 925,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKF\nLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIP\nTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERN\nKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSP\nFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI\nPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI\nPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNT\nDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMR\nDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL\nYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV\nSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI\nLTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN\nVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKI\nLHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE\nCFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG\nVQTLYSKWKDFHFEKIPFDPAEMSK",
"mw": 79.77,
"total_mw": 79.77,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "5´ppp 8mer hairpin dsRNA",
"short_name": "8bp",
"sequence": "GGCGCGGCUUCGGCCGCGCC",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": 1,
"uniprot_range_last": 20,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": null,
"mw": 6.484,
"total_mw": 6.484,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak1)",
"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": "Neelam",
"contributor_surname": "Shah",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-04-27",
"storage_temperature": 4.0,
"cell_temperature": 15.0,
"exposure_time": 5.0,
"number_of_frames": 11,
"wavelength": 0.10332,
"sample_detector_distance": 1.6,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.131,
"s_max": 2.506,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBN8_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "v2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBN8_fit1_model1.pdb",
"model_mw": 77.78,
"bead_radius": null,
"log": null,
"symmetry": "p1",
"comment": "",
"user": 168
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBN8_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "v2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBN8_fit1_model2.pdb",
"model_mw": 77.78,
"bead_radius": null,
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"symmetry": "p1",
"comment": "",
"user": 168
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBN8_fit1_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "v2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBN8_fit1_model3.pdb",
"model_mw": 77.78,
"bead_radius": null,
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"comment": "",
"user": 168
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBN8_fit1_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 0.245,
"p_value": 0.90956,
"fit_residual_plot": "fit4columns680_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBN8_fit1.fit",
"fit_log": null,
"software_version": "v2.1",
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},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBN8_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "v1.1.2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBN8_fit2_model1.pdb",
"model_mw": null,
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}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBN8_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.256,
"p_value": 0.82213,
"fit_residual_plot": "SASDBN8_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBN8_fit2.fir",
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"software_version": "v1.1.2",
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM v4.5",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak1) in 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH 7.4 were collected using size exclusion chromatography (SEC-SAXS) on the SAXS/WAXS camera on the storage ring Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Data frames (11 x 5 s exposures) were collected through the SEC elution peak at 35.1 min (GE Healthcare Life Sciences Superdex 200 10/300; 0.4 ml/min; 50 μl injection at 8 mg/ml). The data were normalized to the intensity of the transmitted beam and radially averaged; the radially averaged scattering of the solvent-blank was subtracted and the different curves were scaled to yield the final composite scattering curve. The SAXS data were collected at 15 °C.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 86.8,
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"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 66.9,
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"pddf_i0": 0.0073,
"pddf_i0_error": null,
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"pddf_dmax": 11.1,
"pddf_dmax_error": null,
"porod_volume": 113.68,
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"estimated_volume": null,
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"guinier_point_first": 13,
"guinier_point_last": 63,
"pddf_point_first": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBN8_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
