{ "code": "SASDEJ3", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/A", "project": { "title": "Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase.", "publication": { "title": "Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase.", "author_list": "Ziegler CS, Bouchab L, Tramier M, Durand D, Fieschi F, Dupré-Crochet S, Mérola F, Nüße O, Erard M", "journal": "J Biol Chem", "doi": "10.1074/jbc.RA118.006864", "pmid": "30630949", "published_date": "2019 Jan 10" }, "status": "released", "submitted_date": "2018-08-28", "released_date": "2019-01-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEJ3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEJ3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEJ3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEJ3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEJ3.sascif", "experiment": { "instrument": { "detector": { "type": "MikroGap gas detector", "name": "VÅNTEC-2000", "resolution": 200.0 }, "name": "IBBMC", "city": "Orsay", "country": "France", "beamline_name": "Bruker Nanostar", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "Neutophil cytosol factor 1", "short_name": "p47phox", "sequence": "GPLGSPNSARMGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEF\r\nHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISR\r\nCPHLLDFFKVRPDDLKLPTDNQTKKPETYLMPKDGKSTATDITGPIILQTYRAIADYEKT\r\nSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEP\r\nYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKSGQDVSQA\r\nQRQIKRGAPPRRSSIRNAHSIHQRSRKRLSQDAYRRNSVRFLQQRRRQARPG", "organism": "Homo sapiens", "uniprot_code": "P14598", "uniprot_range_first": 1, "uniprot_range_last": 342, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPI\nEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISRCPHLLDFFKV\nRPDDLKLPTDNQTKKPETYLMPKDGKSTATDITGPIILQTYRAIANYEKTSGSEMALSTG\nDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAV\nEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKSGQDVSQAQRQIKRGAPP\nRRSSIRNAHSIHQRSRKRLSQDAYRRNSVRFLQQRRRQARPGPQSPGSPLEEERQTQRSK\nPQPAVPPRPSADLILNRCSESTKRKLASAV", "mw": 40.398, "total_mw": 40.398, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 2 mM DTT, 5% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Truncated neutophil cytosol factor 1, p47phox [1-342]", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Paris, France", "full_name": "I2BC-CNRS", "webpage": "http://www.i2bc.paris-saclay.fr" } ], "contributor_name": "Dominique", "contributor_surname": "DURAND", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2009-10-16", "storage_temperature": 6.0, "cell_temperature": 6.0, "exposure_time": 3600.0, "number_of_frames": 11, "wavelength": 0.154, "sample_detector_distance": 0.662, "concentration_min": 0.9, "concentration_max": 3.6, "sample_volume": null, "flow_rate": null, "s_min": 0.142, "s_max": 4.521, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEJ3_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/SASDEJ3_fit1_model1.pdb", "model_mw": 40.4, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 262 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/P47deltaCter_Model00_fit_img.png", "software": "BUNCH", "chi_square_value": 0.971, "p_value": 0.419653, "fit_residual_plot": "fit4columns1676_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEJ3_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/P47deltaCter_Model00.log", "software_version": "08", "description": "p47phoxDCter in solution: \r\nComparison of the experimental data (blue dots) with the calculated scattering pattern (red line) of the BUNCH model shown on the right chi2=0.97. The ultimate adjustment shown here was performed using the program CRYSOL." } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of p47phox [1-342] in 50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 2 mM DTT, 5% glycerol, pH 7.5, were collected on a Bruker Nanostar instrument at the IBBMC (Orsay, France) using a MikroGap VÅNTEC-2000 detector at a sample-detector distance of 0.7 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Samples of were studied at different concentrations ranging from 0.9 to 3.6 mg/ml measured at 6°C. 11 successive 3600 second frames were collected. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program package PRIMUS. Intensities were put on an absolute scale (cm-1) using water scattering. The final pattern used for fitting was obtained by extrapolating to infinite dilution of the set of curves recorded at the different concentrations. Molecular mass was obtained using the bayesian inference approach proposed in PRIMUS/qt, which combines four concentration independent MM estimators: M=39.4 kDa within the credibility interval [36.5-39.8].", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 39.4, "experimental_mw_error": null, "guinier_i0_mw": 38.0, "guinier_i0_mw_error": 4.0, "porod_mw": 38.5, "porod_mw_error": null, "pddf_i0": 0.02836, "pddf_i0_error": 0.0003, "guinier_i0": 0.0287, "guinier_i0_error": 0.0003, "pddf_rg": 2.63, "pddf_rg_error": 0.06, "guinier_rg": 2.64, "guinier_rg_error": 0.06, "pddf_dmax": 10.0, "pddf_dmax_error": 0.5, "porod_volume": 57.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 23, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEJ3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }