{ "code": "SASDCK2", "status": "Published", "type_of_curve": "Other", "angular_unit": "1/A", "project": { "title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.", "publication": { "title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.", "author_list": "Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE", "journal": "Acta Crystallogr D Struct Biol", "doi": "10.1107/S2059798317011597", "pmid": "28876235", "published_date": "2017 Sep 1" }, "status": "released", "submitted_date": "2017-05-06", "released_date": "2017-08-22" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCK2.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK2.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCK2_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCK2.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": "Xylose isomerase", "short_name": "Glucose Isomerase", "sequence": "MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\r\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\r\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\r\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\r\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\r\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\r\nDVDAAAARGMAFERLDQLAMDHLLGARG", "organism": "Streptomyces rubiginosus", "uniprot_code": "P24300", "uniprot_range_first": 1, "uniprot_range_last": 388, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\nDVDAAAARGMAFERLDQLAMDHLLGARG", "mw": 43.227, "total_mw": 172.908, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3", "concentration_unit": null, "comment": "2 mM TCEP and 0.1% (.01538 M) NaN3 used for radiation protection", "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Glucose Isomerase - Streptomyces rubiginosus", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Sydney, New South Wales 2006, Australia", "full_name": "School of Molecular Bioscience, University of Sydney.", "webpage": "" } ], "contributor_name": "Jill", "contributor_surname": "Trewhella", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-03-09", "storage_temperature": null, "cell_temperature": 22.0, "exposure_time": 1.0, "number_of_frames": 24, "wavelength": 0.10332, "sample_detector_distance": 2.683, "concentration_min": 0.06, "concentration_max": 0.34, "sample_volume": null, "flow_rate": null, "s_min": 0.066, "s_max": 3.104, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK2_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "on-line", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK2_fit1_model1.pdb", "model_mw": 120.74, "bead_radius": 2.4, "log": "https://www.sasbdb.org/media/log_files/GIstderr.log", "symmetry": "P1", "comment": "job submitted ATSAS on-line April 9, 2017", "user": 138 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 0.951, "p_value": 0.035, "fit_residual_plot": "SASDCK2_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK2_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/GIstderr.log", "software_version": "on-line", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/GI_tet_img.png", "software": "FoXS", "pdb_link": [ { "pdb_code": "1oad", "ext_code": "1OAD", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": "on-line", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK2_fit2_model1.pdb", "model_mw": 173.7, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "GI tetramer generated from PDB:1OAD using symmetry transforms in pymol", "user": 138 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit2_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 1.02, "p_value": 0.045511, "fit_residual_plot": "SASDCK2_fit2_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK2_fit2.dat", "fit_log": null, "software_version": "on-line", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of glucoes isomerase in 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3, pH 7.5 were collected on the SAXS/WAXS beam line at Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Scattering data are on an absolute scale (cm-1) set by reference to the scattering from pure H2O. I(0) values must be corrected for the shear flow sample cell by a 2.05 multiplicative factor. Data were acquired in SEC-SAXS mode, summed from 21 measurement frames where Rg was flat and at a maximum. The average concentration over the frames was 0.18 mg/mL, spanning values from 0.06 - 0.34 mg/mL. Sample concentrations were measured by A280 (extinction coefficient for 1 mg/mL, 10 mm pathlength; E0.1% = 1.079), corrected for the 3.1 mm path-length of the UV measurement cell. MULCh was used to calculate the partial specific volume (0.732 mL/g) and X-ray contrast (Δρ = 2.833e10 cm-2). The protein is a tetramer in the solution conditions measured.", "tags": [ "benchmark" ], "intensity_unit": "1/cm", "experimental_mw": 172.234, "experimental_mw_error": null, "guinier_i0_mw": 183.254, "guinier_i0_mw_error": null, "porod_mw": 152.667, "porod_mw_error": null, "pddf_i0": 0.03739, "pddf_i0_error": 3.9e-05, "guinier_i0": 0.037, "guinier_i0_error": 4.4e-05, "pddf_rg": 3.265, "pddf_rg_error": 0.004, "guinier_rg": 3.287, "guinier_rg_error": 0.013, "pddf_dmax": 9.22, "pddf_dmax_error": null, "porod_volume": 229.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 43, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCK2_datloglog_img.png", "symmetry": null, "last_modified": "2024-03-08T11:32:18.321280+01:00", "bragg_peak": [] }