{ "code": "SASDF29", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.", "publication": { "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.", "author_list": "Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkz1163", "pmid": "31875226", "published_date": "2019 Dec 25" }, "status": "released", "submitted_date": "2019-07-08", "released_date": "2019-11-29" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF29.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF29.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF29_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF29_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF29_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF29_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF29.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 100K", "resolution": 172.0 }, "name": "CEITEC", "city": "Brno", "country": "Czech Republic", "beamline_name": "Rigaku BioSAXS-1000", "beam_geometry": "", "type_of_source": "X-ray in house", "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": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4", "short_name": "STAU1-RBD4", "sequence": "GSHMNPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK", "organism": "Homo sapiens", "uniprot_code": "O95793", "uniprot_range_first": 286, "uniprot_range_last": 355, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC", "mw": 8.377, "total_mw": 8.377, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "ADP-ribosylation factor1 - short", "short_name": "ARF1 RNA - short", "sequence": "GGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": null, "mw": 10.962, "total_mw": 10.962, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.8, "deuteration": null }, "purity_method": null, "name": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "CEITEC - Central European Institute of Technology, Masaryk University", "webpage": "https://www.ceitec.eu/" } ], "contributor_name": "Tomas", "contributor_surname": "Klumpler", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-12-10", "storage_temperature": 20.0, "cell_temperature": 35.0, "exposure_time": 600.0, "number_of_frames": 6, "wavelength": 0.154, "sample_detector_distance": 0.48, "concentration_min": null, "concentration_max": 6.5, "sample_volume": null, "flow_rate": null, "s_min": 0.483, "s_max": 3.013, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF29_fit1_model1_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CYANA", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF29_fit1_model1.pdb", "model_mw": 384.2, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 195 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF29_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.167, "p_value": 1e-06, "fit_residual_plot": "SASDF29_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF29_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dsRBD4_hARF-for-deposition-2018-11-19_noH-100.log", "software_version": "2.8.3", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 in 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH 6.8 were collected using a Rigaku BioSAXS-1000 instrument (CEITEC; Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.50 mg/ml was measured at 35°C. Six successive 600 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": 15.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 12.938, "porod_mw_error": null, "pddf_i0": 0.4536, "pddf_i0_error": null, "guinier_i0": 0.44, "guinier_i0_error": 0.00043, "pddf_rg": 1.81, "pddf_rg_error": null, "guinier_rg": 1.723, "guinier_rg_error": 0.073, "pddf_dmax": 5.98, "pddf_dmax_error": null, "porod_volume": 20.7, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 19, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF29_datloglog_img.png", "symmetry": null, "last_modified": "2020-02-12T18:29:36.078856+01:00", "bragg_peak": [] }