{ "code": "SASDEK4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.", "publication": { "title": "Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.", "author_list": "Furlong EJ, Kurth F, Premkumar L, Whitten AE, Martin JL", "journal": "Acta Crystallogr D Struct Biol", "doi": "10.1107/S2059798319000081", "pmid": "30950400", "published_date": "2019 Mar 1" }, "status": "released", "submitted_date": "2018-09-18", "released_date": "2019-03-29" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEK4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEK4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEK4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEK4.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": "C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein", "short_name": "PmScsCΔN", "sequence": "SNAQFRQALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQYPDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKSTNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAKVKK", "organism": "Proteus mirabilis", "uniprot_code": "A0A1Z1SYD5", "uniprot_range_first": 64, "uniprot_range_last": 243, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKKTLSVLVISSLLFGANVQAAALNAAQEKEVRALVRDTLVSNPEILEEAIMALQTKKAD\nEQQAQFRQALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQY\nPDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKS\nTNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAK\nVKK", "mw": 20.15, "total_mw": 20.15, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10mM HEPES, 150mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC)", "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": "2018-04-05", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": 1.0, "number_of_frames": 38, "wavelength": 0.1033, "sample_detector_distance": 3.33, "concentration_min": null, "concentration_max": 0.5, "sample_volume": null, "flow_rate": null, "s_min": 0.16, "s_max": 3.634, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEK4_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEK4_fit1_model1.pdb", "model_mw": 16.086, "bead_radius": 1.5, "log": null, "symmetry": "P1", "comment": null, "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/run1_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.079, "p_value": 0.24638, "fit_residual_plot": "run1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEK4_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run1_WKbXguT.log", "software_version": "5.3", "description": "Representative example of 1 of 16 dummy atom modelling optimisations." }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEK4_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "4yx8", "ext_code": "4YX8", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEK4_fit2_model1.pdb", "model_mw": 19.72, "bead_radius": null, "log": null, "symmetry": "P1", "comment": null, "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PmScsCDN01_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.12, "p_value": 0.017618, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEK4_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/PmScsCDN01.log", "software_version": "2.8.3", "description": "" } ], "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 C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC) protein from Proteus mirabilis in 10 mM HEPES 150mM NaCl, pH 7.4 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (s = 4π sin θ/λ, where 2θ is the scattering angle). Thirty eight successive 1 second frames were collected across solute concentrations of 0.1-10.0 mg/ml at a sample temperature of 10°C. The SAXS data displayed this entry was derived from a 0.50 mg/ml sample. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 19.0, "experimental_mw_error": null, "guinier_i0_mw": 11.0, "guinier_i0_mw_error": 2.0, "porod_mw": 19.0, "porod_mw_error": null, "pddf_i0": 0.004053, "pddf_i0_error": null, "guinier_i0": 0.004055, "guinier_i0_error": 1e-06, "pddf_rg": 1.69, "pddf_rg_error": null, "guinier_rg": 1.7, "guinier_rg_error": 0.01, "pddf_dmax": 5.4, "pddf_dmax_error": null, "porod_volume": 22200.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 52, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEK4_datloglog_img.png", "symmetry": null, "last_modified": "2020-06-15T11:37:11.282615+02:00", "bragg_peak": [] }