{ "code": "SASDWJ4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.", "publication": { "title": "Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.", "author_list": "Stafflinger H, Neißner K, Bartsch S, Pichler AK, Bartosik K, Dhamotharan K, Abele R, Duchardt-Ferner E, Micura R, Schindelin H, Wöhnert J", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkaf1315", "pmid": "41422825", "published_date": "2025 Nov 26" }, "status": "released", "submitted_date": "2025-01-13", "released_date": "2025-12-30" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWJ4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWJ4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWJ4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWJ4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWJ4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWJ4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWJ4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 6M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "beam_geometry": null, "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": "Class V GTP aptamer", "short_name": null, "sequence": "GGGCGCAUUUUGGUAGGUCGGUCGCUGCUUCGGCAGUGAGGGGUAGGCAUUGCUGGCCUAGGGUGCCC", "organism": "Escherichia coli", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": "", "mw": 22.116, "total_mw": 22.116, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "Guanosine triphosphate", "short_name": "GTP", "sequence": "C10H16N5O14P3", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "other", "uniprot_sequence": "", "mw": 0.523, "total_mw": 0.523, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "50 mM Bis-Tris, 50 mM KCl, 2 mM MgCl2", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.5, "deuteration": null }, "purity_method": null, "name": "Class V GTP aptamer complex with GTP", "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": "Goethe University Frankfurt, Dept. Biosciences", "webpage": null } ], "contributor_name": "Helena", "contributor_surname": "Stafflinger", "orcid": "https://orcid.org/0009-0006-6219-9942" } ], "concentration_method": null, "concentration_unit": null, "date": "2024-07-19", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.095, "number_of_frames": 40, "wavelength": 0.123985, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 6.0, "sample_volume": null, "flow_rate": null, "s_min": 0.022, "s_max": 7.334, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWJ4_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "3.2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWJ4_fit1_model1.cif", "model_mw": null, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/ClassV6m_1.log", "symmetry": null, "comment": null, "user": 1168 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWJ4_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.216, "p_value": 0.0, "fit_residual_plot": "SASDWJ4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWJ4_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/HSsample04_HSB02_0044_ClassV6m_1-1.log", "software_version": "3.2.1", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWJ4_fit2_model1_img.png", "software": "Coot", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWJ4_fit2_model1.pdb", "model_mw": 22.25, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1168 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWJ4_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 10.774, "p_value": 0.0, "fit_residual_plot": "SASDWJ4_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWJ4_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ClassV_SAXS_HSsample04_HSB02_0044_Ivk1Xix.log", "software_version": "3.2.1", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Class V GTP aptamer complex with GTP in 50 mM Bis-Tris, 50 mM KCl, 2 mM MgCl2, pH 6.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123985 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 mg/ml was measured at 20°C. 40 successive 0.095 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": 24.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 20.4, "porod_mw_error": null, "pddf_i0": 0.09546, "pddf_i0_error": null, "guinier_i0": 0.56766, "guinier_i0_error": null, "pddf_rg": 2.273, "pddf_rg_error": null, "guinier_rg": 2.22, "guinier_rg_error": 0.03, "pddf_dmax": 7.56, "pddf_dmax_error": null, "porod_volume": 33.6, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 67, "guinier_point_last": 201, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDWJ4_datloglog_img.png", "symmetry": null, "last_modified": "2025-12-30T13:43:49.298206+01:00", "bragg_peak": [] }