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{
"code": "SASDBQ3",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering.",
"publication": {
"title": "Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering.",
"author_list": "Papageorgiou N, Lichière J, Baklouti A, Ferron F, Sévajol M, Canard B, Coutard B",
"journal": "Acta Crystallogr D Struct Biol",
"doi": "10.1107/S2059798315024328",
"pmid": "26894667",
"published_date": "2016 Feb"
},
"status": "released",
"submitted_date": "2016-02-09",
"released_date": "2016-02-10"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBQ3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBQ3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBQ3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBQ3.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": "Middle East Respiratory Syndrome (MERS) coronavirus nucleocapsid N-Protein (N-terminal domain 1-164)",
"short_name": "MERS N-Protein",
"sequence": "MASPAAPRAVSFADNNDITNTNLSRGRGRNPKPRAAPNNTVSWYTGLTQHGKVPLTFPPGQGVPLNANSTPAQNAGYWRRQDRKINTGNGIKQLAPRWYFYYTGTGPEAALPFRAVKDGIVWVHEDGATDAPSTFGTRNPNNDSAIVTQFAPGTKLPKNFHIEG",
"organism": "Middle East respiratory syndrome coronavirus",
"uniprot_code": "T2B9R0",
"uniprot_range_first": 1,
"uniprot_range_last": 164,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MASPAAPRAVSFADNNDITNTNLSRGRGRNPKPRAAPNNTVSWYTGLTQHGKVPLTFPPG\nQGVPLNANSTPAQNAGYWRRQDRKINTGNGIKQLAPRWYFYYTGTGPEAALPFRAVKDGI\nVWVHEDGATDAPSTFGTRNPNNDSAIVTQFAPGTKLPKNFHIEGTGGNSQSSSRASSVSR\nNSSRSSSQGSRSGNSTRGTSPGPSGIGAVGGDLLYLDLLNRLQALESGKVKQSQPKVITK\nKDAAAAKNKMRHKRTSTKSFNMVQAFGLRGPGDL",
"mw": 17.788,
"total_mw": 17.788,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM HEPES 300 mM NaCl",
"concentration_unit": "mM",
"comment": null,
"additive": "300 mM NaCl",
"concentration": 10.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Middle East Respiratory Syndrome (MERS) coronavirus nucleocapsid N-Protein (N-terminal domain 1-164)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "13288 Marseille, France",
"full_name": "CNRS, AFMB UMR 7257 ",
"webpage": ""
}
],
"contributor_name": "Nicolas",
"contributor_surname": "Papageorgiou",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2015-10-05",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.93,
"sample_detector_distance": 2.43,
"concentration_min": 0.21,
"concentration_max": 3.06,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.036,
"s_max": 4.975,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBQ3_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r4556",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBQ3_fit1_model1.pdb",
"model_mw": 17.8,
"bead_radius": 1.7,
"log": null,
"symmetry": "",
"comment": "",
"user": 93
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBQ3_fit1_fit_img.png",
"software": null,
"chi_square_value": 0.41,
"p_value": 0.015,
"fit_residual_plot": "SASDBQ3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBQ3_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBQ3_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [
{
"pdb_code": "4ud1",
"ext_code": "4UD1",
"ext_type": "pdb",
"difference_with_model": "other"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBQ3_fit2_model1.pdb",
"model_mw": 17.72,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 93
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBQ3_fit2_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBQ3_fit2_model2.pdb",
"model_mw": 17.72,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 93
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBQ3_fit2_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBQ3_fit2_model3.pdb",
"model_mw": 17.72,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 93
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBQ3_fit2_fit_img.png",
"software": null,
"chi_square_value": 1.982,
"p_value": 4e-06,
"fit_residual_plot": "fit4columns402_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBQ3_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "X-ray synchrotron radiation scattering data from solutions of Middle East Respiratory Syndrome (MERS) coronavirus nucleocapsid N-Protein (N-terminal domain 1-164) in 10 mM HEPES 300 mM NaCl were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a 2D Photon counting Pilatus 1M-W pixel detector (s = 4π sin θ/λ, where 2θ is the scattering angle). Different solute concentrations in the range 0.21-3.06 mg/ml were measured. 10 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected were merged with the highest concentration high angle data to yield the final composite scattering curve. The three models represent the results obtained from ensemble optimisation method (EOM) analysis.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 24.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 26.8,
"pddf_i0_error": null,
"guinier_i0": 26.5,
"guinier_i0_error": null,
"pddf_rg": 2.04,
"pddf_rg_error": null,
"guinier_rg": 1.95,
"guinier_rg_error": null,
"pddf_dmax": 8.0,
"pddf_dmax_error": null,
"porod_volume": 27.5,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 19,
"guinier_point_last": 134,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBQ3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
