{ "code": "SASDDX9", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "mPAC Delta132", "publication": null, "status": "released", "submitted_date": "2018-07-25", "released_date": "2021-09-20" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDX9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDX9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDX9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDX9.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Swiss Light Source", "city": "Villigen", "country": "Switzerland", "beamline_name": "cSAXS", "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": "PAS fold family", "short_name": "mPAC", "sequence": "GAMGSQAYRKGVQETVKLRDQAIAASSVGIVIADARLPDMPLIYVNPAFEEITGYSDAEVLGYNCRFLQGKDTSQPAVDQLRAAIKAGENCTVTLLNYRKDGTPFWNELTISPIYDDHNNLTHFVGIQSDISDRIKAEQALRLEQEKSERLLLNILPKPIVDQLKQFEGSLAQQFTEATILFADIVGFTQLSAQMSPLELLNLLNNIFSVFDKLAEKHGIEKIKTIGDAYMAVAGLPVANDHHAEAIANMALDMQQAIQQFKTPQGEPFQIRIGINTGLVVAGVIGIKKFSYDLWGDAVNVASRMESSGLPGKIQVTAATKERLQDKYVFEKRGAIVVKGKGEMINYWLVGKQE", "organism": "Coleofasciculus chthonoplastes PCC 7420", "uniprot_code": "B4VKN6", "uniprot_range_first": 133, "uniprot_range_last": 483, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MNPSCEENEPNLFHGEASLQAFFDLSAELLCIRDSNGYFREINSVWEKTLGWTLDELRSR\nPWLEFVHPDDVAFTFDMENQCHTLQDNKTPICLKNRFRCRDGSYRWLSWRLGAYQNSVSH\nGIAHDVTESNWRGSQAYRKGVQETVKLRDQAIAASSVGIVIADARLPDMPLIYVNPAFEE\nITGYSDAEVLGYNCRFLQGKDTSQPAVDQLRAAIKAGENCTVTLLNYRKDGTPFWNELTI\nSPIYDDHNNLTHFVGIQSDISDRIKAEQALRLEQEKSERLLLNILPKPIVDQLKQFEGSL\nAQQFTEATILFADIVGFTQLSAQMSPLELLNLLNNIFSVFDKLAEKHGIEKIKTIGDAYM\nAVAGLPVANDHHAEAIANMALDMQQAIQQFKTPQGEPFQIRIGINTGLVVAGVIGIKKFS\nYDLWGDAVNVASRMESSGLPGKIQVTAATKERLQDKYVFEKRGAIVVKGKGEMINYWLVG\nKQE", "mw": 39.015, "total_mw": 78.03, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 5 % w/v Glycerol, 1 mM ApCpp", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "PAS fold family protein mPAC-Δ132 with the addition of adenosine-5'-[(α,β)-methyleno]triphosphate in the dark state (mPAC-Δ132, dark + ApCpp)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Germany", "full_name": "Max Planck Institute for Medical Research", "webpage": "http://www.mpimf-heidelberg.mpg.de/en" } ], "contributor_name": "Robert", "contributor_surname": "Lindner", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2015-03-11", "storage_temperature": 0.0, "cell_temperature": 10.0, "exposure_time": 0.5, "number_of_frames": 200, "wavelength": 0.11, "sample_detector_distance": 2.13, "concentration_min": 5.1, "concentration_max": 9.1, "sample_volume": null, "flow_rate": null, "s_min": 0.16, "s_max": 2.744, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit1_model1_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit1_model1.pdb", "model_mw": 75.06, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 330 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDX9_fit1_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 16.481153, "p_value": 0.0, "fit_residual_plot": "SASDDX9_fit1_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDX9_fit1.dat", "fit_log": null, "software_version": "2", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit2_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.8.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit2_model1.pdb", "model_mw": 59.655, "bead_radius": 3.25, "log": null, "symmetry": null, "comment": null, "user": 330 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit2_model2_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.8.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit2_model2.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 330 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDX9_fit2_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 52.36, "p_value": 0.0, "fit_residual_plot": "SASDDX9_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDX9_fit2.fir", "fit_log": null, "software_version": "2.8.1", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS measurements (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle; λ = 0.11 nm) were carried out at the beam line X12SA of the Swiss Light Source (Paul Scherrer Institut, Villigen, Switzerland). Quartz capillaries (inner diameter 1 mm) were mounted in a sample holder and filled with buffer (20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 5 % w/v glycerol, 1 mM ApCpp, pH 7.5). The sample holder was cooled to 10 °C for all measurements. Scattering of the buffer was determined at 20 positions along the capillary (spacing 0.5 mm), exposing each position with 11.2 keV photons for 0.5 s using 200 successive frames. Each position was measured 10 times and scattering intensities, after radial averaging to produce 1D-scattering patterns, were averaged. Scattered X-rays were detected by a Pilatus 2M detector (Dectris, Baden-Dättwil, Switzerland) at the end of an evacuated flight tube, 2.13 m from the sample position. Buffer was replaced by the protein sample without moving the sample holder or the capillaries. Lights in the experimental hutch were switched off and after 5 minutes, scattering of the protein-containing solutions was measured at the same positions using the procedure described above. Solute concentrations ranging between 5.1 and 9.1 mg/ml were measured and the concentration series data extrapolated to infinite dilution generating the final SAXS profile displayed in this entry. GASBOR was run 10 times to generate bead-model reconstructions (an averaged representation, top, and individual model, bottom).", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 83.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 7.849, "pddf_i0_error": null, "guinier_i0": 8.29, "guinier_i0_error": 0.017, "pddf_rg": 3.81, "pddf_rg_error": null, "guinier_rg": 3.95, "guinier_rg_error": 0.19, "pddf_dmax": 12.8, "pddf_dmax_error": null, "porod_volume": 99.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 12, "guinier_point_last": 35, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDX9_datloglog_img.png", "symmetry": null, "last_modified": "2021-09-20T13:38:19.096872+02:00", "bragg_peak": [] }