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{
"code": "SASDDY4",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions.",
"publication": {
"title": "A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions.",
"author_list": "Chen PC, Masiewicz P, Rybin V, Svergun D, Hennig J",
"journal": "ACS Comb Sci",
"doi": "10.1021/acscombsci.8b00007",
"pmid": "29553252",
"published_date": "2018 Apr 9"
},
"status": "released",
"submitted_date": "2018-03-15",
"released_date": "2018-03-21"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDY4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDY4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDY4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDY4.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": "Protein sex-lethal mutant",
"short_name": "Sxl10GS",
"sequence": ">P19339 Sxl-mutant 123-294 with GAMA cleavage site and 10GS linker inserted between 204-205\r\nGAMASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQ\r\nRAIKVLNGITVRNKRLKVSYARPGGGSGSGGGGSGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK\r\nNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAEEHGK",
"organism": "Drosophila melanogaster",
"uniprot_code": "P19339",
"uniprot_range_first": 123,
"uniprot_range_last": 294,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MYGNNNPGSNNNNGGYPPYGYNNKSSGGRGFGMSHSLPSGMSRYAFSPQDTEFSFPSSSS\nRRGYNDFPGCGGSGGNGGSANNLGGGNMCHLPPMASNNSLNNLCGLSLGSGGSDDLMNDP\nRASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQ\nRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK\nNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAEEHGKAKAAHF\nMSQMGVVPANVPPPPPQPPAHMAAAFNMMHRGRSIKSQQRFQNSHPYFDAKKFI",
"mw": 20.432,
"total_mw": 20.432,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM KP, 50 mM NaCl, 10 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.0,
"deuteration": null
},
"purity_method": null,
"name": "Protein sex-lethal mutant with 10GS-linker",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL",
"address": "Heidelberg, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Heidelberg",
"webpage": "https://www.embl.de/"
}
],
"contributor_name": "Po-chia",
"contributor_surname": "Chen",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-02-02",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.09919,
"sample_detector_distance": 2.867,
"concentration_min": null,
"concentration_max": 1.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.035,
"s_max": 4.942,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY4_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY4_fit1_model1.pdb",
"model_mw": 20.05,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY4_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY4_fit1_model2.pdb",
"model_mw": 20.05,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY4_fit1_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY4_fit1_model3.pdb",
"model_mw": 20.05,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY4_fit1_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY4_fit1_model4.pdb",
"model_mw": 20.05,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY4_fit1_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY4_fit1_model5.pdb",
"model_mw": 20.05,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDY4_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.642,
"p_value": 0.675072,
"fit_residual_plot": "fit4columns1338_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDY4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/mut-apo_eom.log",
"software_version": "2.1",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.5a",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Protein sex-lethal mutant with 10GS-linker in 10 mM KP, 50 mM NaCl, 10 mM DTT, pH 6 were collected 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 = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.00 mg/ml was measured at 20°C. 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 16.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 15.85,
"porod_mw_error": null,
"pddf_i0": 22.77,
"pddf_i0_error": 0.05,
"guinier_i0": 22.66,
"guinier_i0_error": 0.02,
"pddf_rg": 2.18,
"pddf_rg_error": 0.009,
"guinier_rg": 2.12,
"guinier_rg_error": 0.05,
"pddf_dmax": 7.4,
"pddf_dmax_error": null,
"porod_volume": 26.95,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 121,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDY4_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:59.340668+02:00",
"bragg_peak": []
}
