{ "code": "SASDF59", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Self association of LIM domain binding protein 1, LDB1", "publication": null, "status": "released", "submitted_date": "2019-07-16", "released_date": "2021-09-27" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF59.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF59.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF59_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF59_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF59_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF59_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF59.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": "LIM domain-binding protein 1", "short_name": "LDB1", "sequence": ">LDB1 WT 14-200\r\nGELGSPTYLEPGIGRHTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIGRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLS", "organism": "Mus musculus", "uniprot_code": "P70662", "uniprot_range_first": 14, "uniprot_range_last": 200, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MSVGCACPGCSSKSFKLYSPKEPPNGNAFPPFHPGTMLDRDVGPTPMYPPTYLEPGIGRH\nTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIG\nRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEG\nRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLSNSTL\nNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPARQQPSKRRKRK\nMSGGSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITR\nLENTQFDAANGIDDEDSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ", "mw": 22.58, "total_mw": 45.16, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 150 mM NaCl, 1 mM TCEP,", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "LIM domain-binding protein 1 (Ldb1) self association domain", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Sydney, Australia", "full_name": "School of Life and Environmental Science, University of Sydney", "webpage": "http://sydney.edu.au/science/life-environment/" } ], "contributor_name": "Jacqueline", "contributor_surname": "Matthews", "orcid": "https://orcid.org/0000-0001-8518-3472" } ], "concentration_method": null, "concentration_unit": null, "date": "2015-11-19", "storage_temperature": 22.0, "cell_temperature": 13.6, "exposure_time": 1.0, "number_of_frames": 24, "wavelength": 0.10332, "sample_detector_distance": 2.68, "concentration_min": null, "concentration_max": 0.4, "sample_volume": null, "flow_rate": null, "s_min": 0.064, "s_max": 3.277, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF59_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF59_fit1_model1.pdb", "model_mw": 32.65, "bead_radius": null, "log": null, "symmetry": null, "comment": "The asymmetric unit is monomeric with 2 dimers by symmetry. Missing ~30% density.", "user": 466 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF59_fit1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 1.09, "p_value": 0.048391, "fit_residual_plot": "SASDF59_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF59_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/2CorHHD6.log", "software_version": "05", "description": "HH model. CORAL calculations where performed for each measured data set with each of the two potential crystal structure dimers held fixed, while the missing termini and loop fragments were free to be optimised. In every case, the head-to-head (HH) dimer based structure was able to fit the data significantly better than that of the head-to-tail (HT) dimer." }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF59_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF59_fit2_model1.pdb", "model_mw": 32.65, "bead_radius": null, "log": null, "symmetry": null, "comment": "The asymmetric unit is monomeric with 2 dimers by symmetry. Missing ~30% density.", "user": 466 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF59_fit2_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 1.56, "p_value": 0.0, "fit_residual_plot": "SASDF59_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF59_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/2CorHTD6.log", "software_version": "5", "description": "HT CORAL calculations where performed for each measured data set with each of the two potential crystal structure dimers held fixed, while the missing termini and loop fragments were free to be optimised. In every case, the head-to-head (HH) dimer based structure was able to fit the data significantly better than that of the head-to-tail (HT) dimer" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "A five point concentration series was collected at the Australian Synchrotron and reduced to I(s) versus s. Parameters derived from the Guinier analysis showed a small concentration dependence of systematically increasing molecular mass (M) values from I(0). The M values were consistent with a predominantly dimeric for for all samples, the data suggest there may be somewhat less than complete dimerization at the lower concentration values, and potentially some further associations at the highest concentration values. Data is provided for the sample at 0.4 mg/ml where the M value is consistent with dimer.", "experiment_description": "Synchrotron SAXS data from solutions Ldb1 self association domain in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.40 mg/ml was measured at 13.6°C. 24 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 45.161, "experimental_mw_error": null, "guinier_i0_mw": 45.23, "guinier_i0_mw_error": null, "porod_mw": 50.0, "porod_mw_error": null, "pddf_i0": 0.01298, "pddf_i0_error": null, "guinier_i0": 0.01299, "guinier_i0_error": null, "pddf_rg": 2.5, "pddf_rg_error": null, "guinier_rg": 2.49, "guinier_rg_error": 0.08, "pddf_dmax": 8.8, "pddf_dmax_error": null, "porod_volume": 79.5, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 10, "guinier_point_last": 118, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF59_datloglog_img.png", "symmetry": null, "last_modified": "2021-09-27T16:29:14.069594+02:00", "bragg_peak": [] }