{ "code": "SASDCL8", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "WAXS benchmark on standard proteins", "publication": null, "status": "released", "submitted_date": "2017-10-17", "released_date": "2021-09-13" }, "pddf_data": null, "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCL8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL8_kratky_img.png", "pddf_plot": null, "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCL8.sascif", "experiment": { "instrument": { "detector": { "type": "Custom-built", "name": "Pilatus 1M-W", "resolution": 0.172 }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "beam_geometry": "Point", "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": "Myoglobin", "short_name": null, "sequence": ">sp|P68082|MYG_HORSE Myoglobin OS=Equus caballus GN=MB PE=1 SV=2\nMGLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASE\nDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKH\nPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG\n\n", "organism": "Equus caballus", "uniprot_code": "P68082", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASE\nDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKH\nPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG", "mw": 17.08, "total_mw": 17.0, "number_molecules": 1, "complex_state": null, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "100 mM tris pH 7.5, 100 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Horse myoglobin (WAXS)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Maxim", "contributor_surname": "Petoukhov", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-06-02", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 0.2, "number_of_frames": 54, "wavelength": 0.062, "sample_detector_distance": null, "concentration_min": null, "concentration_max": 5.2, "sample_volume": null, "flow_rate": null, "s_min": 0.199, "s_max": 25.559, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCL8_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "1npf", "ext_code": "1NPF", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCL8_fit1_model1.pdb", "model_mw": 17.71, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 102 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCL8_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 5.377, "p_value": 0.0, "fit_residual_plot": "SASDCL8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCL8_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/1npf04.log", "software_version": "crysol 3.0", "description": null } ], "estimated_volume_method": null, "pddf_software": null, "pddf_software_version": null, "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of horse myoglobin (WAXS) in 100 mM Tris, 100 mM NaCl, pH 7.5 were collected on the EMBL-P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 1M-W detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.062 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.20 mg/ml was measured at 10°C. 54 successive 0.200 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 and the data scaled to protein concentration.", "tags": [ "benchmark" ], "intensity_unit": "arbitrary", "experimental_mw": 17.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": null, "pddf_i0_error": null, "guinier_i0": 1068.23, "guinier_i0_error": 1.21, "pddf_rg": null, "pddf_rg_error": null, "guinier_rg": 1.6, "guinier_rg_error": null, "pddf_dmax": null, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 59, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCL8_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:18.120449+02:00", "bragg_peak": [] }