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{
"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": []
}
