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{
"code": "SASDD25",
"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/SASDD25.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD25.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD25_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD25_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD25_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD25_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD25.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": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MYGNNNPGSNNNNGGYPPYGYNNKSSGGRGFGMSHSLPSGMSRYAFSPQDTEFSFPSSSS\nRRGYNDFPGCGGSGGNGGSANNLGGGNMCHLPPMASNNSLNNLCGLSLGSGGSDDLMNDP\nRASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQ\nRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK\nNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAEEHGKAKAAHF\nMSQMGVVPANVPPPPPQPPAHMAAAFNMMHRGRSIKSQQRFQNSHPYFDAKKFI",
"mw": 20.432,
"total_mw": 40.864,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "RNA decaneucleotide UGU8",
"short_name": "UGU8",
"sequence": "> Synthetic RNA UGU8\r\nUGUUU UUUUU",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "RNA",
"uniprot_sequence": null,
"mw": 3.119,
"total_mw": 6.238,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50% dilution of protein buffer {10 mM KP, 50 mM NaCl, 10 mM DTT pH 6} with {milliQ-water pH 7} suspended RNA",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.0,
"deuteration": null
},
"purity_method": null,
"name": "1:1 Mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide UGU8",
"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": "2017-04-12",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 0.5,
"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": 0.031,
"s_max": 4.944,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD25_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/SASDD25_fit1_model1.pdb",
"model_mw": 46.25,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD25_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/SASDD25_fit1_model2.pdb",
"model_mw": 46.25,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD25_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/SASDD25_fit1_model3.pdb",
"model_mw": 46.25,
"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/SASDD25_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.446,
"p_value": 0.240677,
"fit_residual_plot": "fit4columns1340_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD25_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/mut-UGU8_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": "This synchrotron session suffered from misalignment of the beamstop resulting in parasitic scattering at low angles. Note that the uploaded EOM ensemble is chosen as the 2:2-complex with one RNA monomer as fully bound by two Sxl10GS molecules in the canonical position from Protein data bankk (PDB) entry 1B7F.pdb. The second RNA monomer is placed in the canonical position bound to the free RRM2, resulting in three rigid bodies: RRM2+RNA, RRM1+RRM2+RNA, and RRM1.",
"experiment_description": "Synchrotron SAXS data from solutions of a 1:1 mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide UGU8 in 50% dilution of protein buffer (10 mM KP, 50 mM NaCl, 10 mM DTT), pH 6 were collected on the BM29 beam line at the ESRF storage ring (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 0.500 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": 24.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 77.67,
"pddf_i0_error": 0.08,
"guinier_i0": 76.65,
"guinier_i0_error": 0.13,
"pddf_rg": 2.63,
"pddf_rg_error": 0.004,
"guinier_rg": 2.54,
"guinier_rg_error": 0.07,
"pddf_dmax": 8.88,
"pddf_dmax_error": null,
"porod_volume": 40.96,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 51,
"guinier_point_last": 92,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD25_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:59.704255+02:00",
"bragg_peak": []
}
