{ "code": "SASDCC8", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.", "publication": { "title": "Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.", "author_list": "Meier M, Moya-Torres A, Krahn NJ, McDougall MD, Orriss GL, McRae EKS, Booy EP, McEleney K, Patel TR, McKenna SA, Stetefeld J", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gky307", "pmid": "29718405", "published_date": "2018 Jun 1" }, "status": "released", "submitted_date": "2017-10-10", "released_date": "2018-05-01" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCC8.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCC8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCC8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCC8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCC8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCC8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCC8.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "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": "Human telomerase RNA template component, DNA counterpart, nucleotides 1-20", "short_name": "TERC DNA", "sequence": "GGGTTGCGGAGGGTGGGCCT", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": 1, "uniprot_range_last": 20, "oligomerization": "dimer", "molecular_type": "DNA", "uniprot_sequence": null, "mw": 6.366, "total_mw": 12.732, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES, 100 mM KCl,", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Human TERC 1-20 DNA G-quadruplex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Winnipeg, Canada", "full_name": "University of Manitoba", "webpage": "http://umanitoba.ca/" } ], "contributor_name": "Markus", "contributor_surname": "Meier", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-08-02", "storage_temperature": 4.0, "cell_temperature": 25.0, "exposure_time": 3.0, "number_of_frames": 9, "wavelength": 0.1, "sample_detector_distance": 4.014, "concentration_min": 2.0, "concentration_max": 2.0, "sample_volume": null, "flow_rate": null, "s_min": 0.059, "s_max": 3.898, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCC8_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r9678", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCC8_fit1_model1.pdb", "model_mw": null, "bead_radius": 1.25, "log": "https://www.sasbdb.org/media/log_files/004_3_MM_p1_shape_compact-hollow_dammin_expert.log", "symmetry": "P1", "comment": "Fixed core calculated from 20 dammif models using compact-hollow shape assumption", "user": 210 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCC8_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.346, "p_value": 0.003043, "fit_residual_plot": "SASDCC8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCC8_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/004_3_MM_p1_shape_compact-hollow_dammin_expert.log", "software_version": "r9678", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCC8_fit2_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r9678", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCC8_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.25, "log": "https://www.sasbdb.org/media/log_files/004_3_MM_p1_shape_compact_dammin_expert_UzSfNku.log", "symmetry": "P1", "comment": "Fixed core calculated from 20 dammif models using compact shape assumption.", "user": 210 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCC8_fit2_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.346, "p_value": 0.003043, "fit_residual_plot": "SASDCC8_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCC8_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/004_3_MM_p1_shape_compact_dammin_expert.log", "software_version": "r9678", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCC8_fit3_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r9678", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCC8_fit3_model1.pdb", "model_mw": null, "bead_radius": 1.25, "log": "https://www.sasbdb.org/media/log_files/004_3_MM_p1_shape_unknown_dammin_expert.log", "symmetry": "P1", "comment": "Fixed core calculated from 20 dammif models using unknown shape assumption.", "user": 210 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCC8_fit3_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.346, "p_value": 0.003043, "fit_residual_plot": "SASDCC8_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCC8_fit3.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/004_3_MM_p1_shape_unknown_dammin_expert.log", "software_version": "r9678", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "r9678", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SEC-SAXS data collection was performed at the B21 beamline of the Diamond Light Source (UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). 50 µl purified hTERC 1-20 DNA G-quadruplex at a concentration of 5.58 mg/ml was injected into a 4.6 ml Shodex KW402.5-4F size exclusion column at a flow rate of 0.16 ml/min that was connected to the SAXS flow cell (25°C). The column diluted the sample 3-fold to approximately 2 mg/ml. Each frame was exposed for 3 seconds. 9 frames of the sample peak region were integrated, buffer subtracted and merged using the ScÅtter software package (http://www.bioisis.net/scatter). Guinier Rg, I(0) and their standard uncertainties were determined with GNOM/DATRG from ATSAS suite 2.8.2 (https://www.embl-hamburg.de/biosaxs/software.html). The Porod volume was calculated with DATPOROD from the ATSAS suite. The molecular weight derived from I(0) was calculated with SAXSMoW2 (http://saxs.ifsc.usp.br) and corrected for the appropriate mass density of the G-quadruplex DNA (1.85 g/cm³).", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 14.14, "experimental_mw_error": null, "guinier_i0_mw": 14.14, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.0547, "pddf_i0_error": 3e-05, "guinier_i0": 0.05469, "guinier_i0_error": 3e-05, "pddf_rg": 1.419, "pddf_rg_error": 0.002, "guinier_rg": 1.42, "guinier_rg_error": 0.001, "pddf_dmax": 4.62, "pddf_dmax_error": null, "porod_volume": 15.1, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 36, "guinier_point_last": 450, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCC8_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }