{ "code": "SASDDM6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "The X-ray structure of human calbindin-D28K: an improved model.", "publication": { "title": "The X-ray structure of human calbindin-D28K: an improved model.", "author_list": "Noble JW, Almalki R, Roe SM, Wagner A, Duman R, Atack JR", "journal": "Acta Crystallogr D Struct Biol", "doi": "10.1107/S2059798318011610", "pmid": "30289411", "published_date": "2018 Oct 1" }, "status": "released", "submitted_date": "2018-05-17", "released_date": "2018-10-04" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDM6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDM6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDM6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDM6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDM6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDM6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDM6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "type_of_source": "X-ray synchrotron", "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": "Calbindin", "short_name": "CALB1", "sequence": "GPHMAESHLQSSLITASQFFEIWLHFDADGSGYLEGKELQNLIQELQQARKKAGLELSPEMKTFVDQYGQRDDGKIGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKYDTDHSGFIETEELKNFLKDLLEKANKTVDDTKLAEYTDLMLKLFDSNNDGKLELTEMARLLPVQENFLLKFQGIKMCGKEFNKAFELYDQDGNGYIDENELDALLKDLCEKNKQDLDINNITTYKKNIMALSDGGKLYRTDLALILCAGDN", "organism": "Homo sapiens", "uniprot_code": "P05937", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MAESHLQSSLITASQFFEIWLHFDADGSGYLEGKELQNLIQELQQARKKAGLELSPEMKT\nFVDQYGQRDDGKIGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKYDTDHSGFIET\nEELKNFLKDLLEKANKTVDDTKLAEYTDLMLKLFDSNNDGKLELTEMARLLPVQENFLLK\nFQGIKMCGKEFNKAFELYDQDGNGYIDENELDALLKDLCEKNKQDLDINNITTYKKNIMA\nLSDGGKLYRTDLALILCAGDN", "mw": 30.316, "total_mw": 30.316, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 150mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.8, "deuteration": null }, "purity_method": null, "name": "Calbindin-D28K", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Brighton, UK", "full_name": "University of Sussex", "webpage": "http://www.sussex.ac.uk/" } ], "contributor_name": "James", "contributor_surname": "Noble", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2018-02-28", "storage_temperature": 4.0, "cell_temperature": 25.0, "exposure_time": 3.0, "number_of_frames": 14, "wavelength": 0.1, "sample_detector_distance": 4.0, "concentration_min": null, "concentration_max": 12.2, "sample_volume": null, "flow_rate": null, "s_min": 0.037, "s_max": 3.696, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDM6_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "dammif", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDM6_fit1_model1.pdb", "model_mw": 27.6, "bead_radius": 2.5, "log": null, "symmetry": null, "comment": null, "user": 280 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDM6_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.156, "p_value": 0.172169, "fit_residual_plot": "SASDDM6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDM6_fit1.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.5a", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of calbindin-D28K in 20 mM Tris, 150mM NaCl, pH 7.8, were collected on the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 12.20 mg/ml was measured at 25°C. 14 successive 3 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": "arbitrary", "experimental_mw": 25.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 29.0, "porod_mw_error": null, "pddf_i0": 0.08571, "pddf_i0_error": null, "guinier_i0": 0.08563, "guinier_i0_error": 0.0001, "pddf_rg": 2.14, "pddf_rg_error": null, "guinier_rg": 2.142, "guinier_rg_error": 0.005, "pddf_dmax": 6.95, "pddf_dmax_error": null, "porod_volume": 46.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 38, "guinier_point_last": 259, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDM6_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }