{ "code": "SASDBG6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate.", "publication": { "title": "Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate.", "author_list": "Zhang J, Gonzalez LE, Hall TMT", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkw961", "pmid": "27789691", "published_date": "2017 Mar 17" }, "status": "released", "submitted_date": "2016-09-18", "released_date": "2017-04-05" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBG6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBG6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBG6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBG6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "MAR 165 CCD", "resolution": null }, "name": "Advanced Light Source (ALS)", "city": "Berkeley, CA", "country": "USA", "beamline_name": "12.3.1 (SIBYLS)", "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": "Ribosome biogenesis protein 15", "short_name": "Nop15", "sequence": "KDKKTLEEYS GIIYVSRLPH GFHEKELSKY FAQFGDLKEV RLARNKKTGN SRHYGFLEFV NKEDAMIAQE \r\nSMNNYLLMGH LLQVRVLPKG AKIEKLYKYK KRVLVEKGIT KPVKQLKDNMKQKHEERIKK LAKSGIEFKW", "organism": "Saccharomyces cerevisiae", "uniprot_code": "P53927", "uniprot_range_first": 81, "uniprot_range_last": 220, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MVKSTSKTSTKETVTKQPTEEKPIQEKEELALETSSSSSDEEDEKDEDEIEGLAASDDEQ\nSGTHKIKRLNPKKQANEKKSKDKKTLEEYSGIIYVSRLPHGFHEKELSKYFAQFGDLKEV\nRLARNKKTGNSRHYGFLEFVNKEDAMIAQESMNNYLLMGHLLQVRVLPKGAKIEKLYKYK\nKRVLVEKGITKPVKQLKDNMKQKHEERIKKLAKSGIEFKW", "mw": 16.541, "total_mw": 16.541, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM HEPES, 500 mM NaCl, 2 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Ribosome biogenesis protein 15 (Nop15)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "NIH", "address": "Bethesda, Maryland, USA", "full_name": "National Institutes of Health, Bethesda, MD", "webpage": "https://www.nih.gov/" } ], "contributor_name": "Jun", "contributor_surname": "Zhang", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2013-04-25", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 0.5, "number_of_frames": 1, "wavelength": 0.1, "sample_detector_distance": null, "concentration_min": 0.7, "concentration_max": 3.0, "sample_volume": null, "flow_rate": null, "s_min": 0.198, "s_max": 2.934, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG6_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [ { "pdb_code": "5t9p", "ext_code": "5T9P", "ext_type": "pdb", "difference_with_model": "other" } ], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG6_fit1_model1.pdb", "model_mw": 15.99, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/logFile_001_1.log", "symmetry": "", "comment": "", "user": 157 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG6_fit1_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG6_fit1_model2.pdb", "model_mw": 15.99, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/logFile_001_1_D8AznaA.log", "symmetry": "", "comment": "", "user": 157 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG6_fit1_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG6_fit1_model3.pdb", "model_mw": 15.99, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/logFile_001_1_6M5amPg.log", "symmetry": "", "comment": "", "user": 157 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBG6_fit1_fit_img.png", "software": null, "chi_square_value": 0.649, "p_value": 0.0, "fit_residual_plot": "fit4columns497_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBG6_fit1.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM 5", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of ribosome biogenesis protein 15 (Nop15) in 25 mM HEPES, 500 mM NaCl, 2 mM DTT, pH 7.5 were collected on the BL 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS, Berkeley, CA, USA) using a MAR Image Plate detector at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.7 and 3 mg/ml were measured at 4 °C (the data displayed in this entry: 0.7 mg/ml). One 0.5 second frame was collected per sample. The data were normalized to the intensity of the transmitted beam, radially averaged and the scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": null, "experimental_mw": 16.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 23.0, "porod_mw_error": null, "pddf_i0": 125.6, "pddf_i0_error": 3.5, "guinier_i0": 113.76, "guinier_i0_error": 3.6, "pddf_rg": 2.86, "pddf_rg_error": 0.09, "guinier_rg": 2.4, "guinier_rg_error": 0.09, "pddf_dmax": 10.3, "pddf_dmax_error": null, "porod_volume": 38.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 27, "guinier_point_last": 56, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBG6_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }