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{
"code": "SASDDZ4",
"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/SASDDZ4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDZ4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDZ4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDZ4.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
},
{
"long_name": "RNA decaneucleotide U8GU",
"short_name": "U8GU",
"sequence": "> Synthetic RNA U8GU\r\nUUUUU UUUGU",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": null,
"mw": 3.119,
"total_mw": 3.119,
"number_molecules": 1,
"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 U8GU",
"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": "2017-02-03",
"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/SASDDZ4_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/SASDDZ4_fit1_model1.pdb",
"model_mw": 23.14,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ4_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/SASDDZ4_fit1_model2.pdb",
"model_mw": 23.14,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ4_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/SASDDZ4_fit1_model3.pdb",
"model_mw": 23.14,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ4_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/SASDDZ4_fit1_model4.pdb",
"model_mw": 23.14,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ4_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/SASDDZ4_fit1_model5.pdb",
"model_mw": 23.14,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 297
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ4_fit1_model6_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/SASDDZ4_fit1_model6.pdb",
"model_mw": 23.14,
"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/SASDDZ4_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.776,
"p_value": 0.016952,
"fit_residual_plot": "fit4columns1339_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDZ4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/mut-U8GU_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": "Note that the uploaded EOM ensemble is chosen as the 1:1-complex with U8GU positioned in the canonical RRM2 at 5' position from the Protein data bank (PDB) entry 1B7F.pdb. There is no observable discrimination between whether RRM1 or RRM2 is bound or its position along the RNA sequence.",
"experiment_description": "Synchrotron SAXS data from solutions of a 1:1 mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide U8GU in 50% dilution of protein buffer (10 mM KH2PO4, 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 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": 20.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 42.07,
"pddf_i0_error": 0.05,
"guinier_i0": 41.98,
"guinier_i0_error": 0.048,
"pddf_rg": 2.29,
"pddf_rg_error": 0.005,
"guinier_rg": 2.24,
"guinier_rg_error": 0.49,
"pddf_dmax": 7.79,
"pddf_dmax_error": null,
"porod_volume": 34.26,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 32,
"guinier_point_last": 116,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDZ4_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:59.545272+02:00",
"bragg_peak": []
}
