{ "code": "SASDCH7", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.", "publication": { "title": "Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.", "author_list": "Smith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B", "journal": "Acta Crystallogr F Struct Biol Commun", "doi": "10.1107/S2053230X17017800", "pmid": "29372905", "published_date": "2018 Jan 1" }, "status": "released", "submitted_date": "2017-09-13", "released_date": "2018-01-03" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCH7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCH7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCH7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCH7.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "SAXS/WAXS", "beam_geometry": "Point", "type_of_source": "X-ray synchrotron", "point_source": true, "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": "N-terminus of disulfide interchange protein DsbD", "short_name": "n-DsbD", "sequence": "SNANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAKIVGKTDPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGCAEVGVCYPPVDTEFDISGNGTYHPQT", "organism": "Neisseria meningitidis", "uniprot_code": "Q9JTL9", "uniprot_range_first": 23, "uniprot_range_last": 146, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKKLICLFAVFLMLCGRAFALDANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAK\nIVGKTDPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGC\nAEAGVCYPPVDTEFDISGNGTYHPQTDEPASAKDRFLQPSSQNGSGALPPPKGDEGGDSR\nFKLSWDTLNANLLAFFLAGLGLSFTACMYPLLPIVSSIVVGDKKAGKARAFVLSVVYVQG\nLSLTYTLVGIVAGLTGALLTVWLQQAWVVLAASALMVVLALSMFGLFNIQLPNAVQSYFQ\nNQSSRLSGGKIVSVFIMGILSALIVGPCVAPPLAFALGYIGQTGDAVLGGLALYTLALGT\nGVPLIAIGTFGGHILPRAGDWMNAVKYAFGFILLAVAVYLATPHLPYYLVVALYTLLMLV\nPACMLLVNGRRQKRRPKAVAFALGGILLIGGAWFGWQGANGKTTALHHFLTLNPPAEAGK\nSSEHGKMFADTAALKAAMDTALKEHPDKPVVLDFYADWCISCKEMAAYTLNQPEVHQAVD\nMERFFQIDVTANTPEHQALLKEYGLFGPPGVFVVRSDGSRSEPLLGFVKADKFIEWYEQN\nR", "mw": 13.911, "total_mw": 13.911, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25mM HEPES 150mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.7, "deuteration": null }, "purity_method": null, "name": "N-terminal domain of DsbD from N. meningitidis", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "ANSTO", "address": "Kirrawee DC, NSW 2232, Australia", "full_name": "Australian Nuclear Science and Technology Organisation", "webpage": "" } ], "contributor_name": "Andrew", "contributor_surname": "Whitten", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2013-05-04", "storage_temperature": 4.0, "cell_temperature": 12.0, "exposure_time": 2.0, "number_of_frames": 30, "wavelength": 0.1127, "sample_detector_distance": 1.48, "concentration_min": 0.4, "concentration_max": 5.9, "sample_volume": null, "flow_rate": null, "s_min": 0.136, "s_max": 3.99, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCH7_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCH7_fit1_model1.pdb", "model_mw": 12.131, "bead_radius": 1.5, "log": "https://www.sasbdb.org/media/log_files/damsel_ZE5wX89.log", "symmetry": "", "comment": "", "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCH7_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.899, "p_value": 0.0, "fit_residual_plot": "SASDCH7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCH7_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run3.log", "software_version": "5.3", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "X-ray synchrotron radiation scattering data from solutions of the n-terminal domain of DsbD from Neisseria meningitidis in 25 mM HEPES 150mM NaCl pH 6.7 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.1127 nm). Thirty successive 2 second frames were collected across solute concentrations of 0.4-5.9 mg/ml. The SAXS data displayed this entry was derived from a 0.74 mg/ml sample as it was deemed to be the highest concentration at which the effects of concentration were negligible. The Rg for n-NmDsbD showed mild concentration dependence above a concentration of 1.0 mg/mL, dropping from ~17.5 Å at 0.4 mg/mL to ~16 Å at 5.9 mg/mL. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 13.2, "experimental_mw_error": null, "guinier_i0_mw": 13.2, "guinier_i0_mw_error": 1.0, "porod_mw": 14.2, "porod_mw_error": null, "pddf_i0": 0.007688, "pddf_i0_error": 1.2e-05, "guinier_i0": 0.00776, "guinier_i0_error": 3e-05, "pddf_rg": 1.73, "pddf_rg_error": 0.1, "guinier_rg": 1.76, "guinier_rg_error": 0.02, "pddf_dmax": 5.7, "pddf_dmax_error": 0.3, "porod_volume": 17.3, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 3, "guinier_point_last": 37, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCH7_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }