The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDDQ4",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/A",
"project": {
"title": "Mutation in a flexible linker modulates binding affinity for modular complexes.",
"publication": {
"title": "Mutation in a flexible linker modulates binding affinity for modular complexes.",
"author_list": "Stokes PH, Robertson NO, Silva AP, Estephan T, Trewhella J, Guss JM, Matthews JM",
"journal": "Proteins",
"doi": "10.1002/prot.25675",
"pmid": "30788856",
"published_date": "2019 Feb 20"
},
"status": "released",
"submitted_date": "2017-09-27",
"released_date": "2019-03-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDQ4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDQ4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDQ4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDQ4.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/homeobox protein Lhx4",
"short_name": "Lhx4-LIM domains",
"sequence": "GSMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQ",
"organism": "Mus musculus",
"uniprot_code": "P53776",
"uniprot_range_first": 24,
"uniprot_range_last": 149,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MMQSAAVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADC\nQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIIC\nNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSP\nKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGGSKQ\nEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQ\nDLRDGSPYGIPQSPSSISSLPSHAPLLNGLDYTVDSNLGIIAHAGQGVSQTLRAMAGGPT\nSDLSTGSSVGYPDFPTSPASWLDEMDHPPF",
"mw": 14.712,
"total_mw": 14.712,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Insulin gene enhancer protein ISL-2",
"short_name": "ISL-2",
"sequence": "GGSGGHMGSGGGTPLVAGSPIRHENAVQGSAVEVQTYQPPW",
"organism": "Mus musculus",
"uniprot_code": "Q9CXV0",
"uniprot_range_first": 273,
"uniprot_range_last": 301,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MVDIIFHYPFLGAMGDHSKKKPGTAMCVGCGSQIHDQFILRVSPDLEWHAACLKCAECSQ\nYLDETCTCFVRDGKTYCKRDYVRLFGIKCAQCQVGFSSSDLVMRARDSVYHIECFRCSVC\nSRQLLPGDEFSLREHELLCRADHGLLLERAAAGSPRSPGPLPGARGLHLPDAGSGRQPSL\nRTHVHKQAEKTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQ\nNKRCKDKKKSILMKQLQQQQHSDKASLQGLTGTPLVAGSPIRHENAVQGSAVEVQTYQPP\nWKALSEFALQSDLDQPAFQQLVSFSESGSLGNSSGSDVTSLSSQLPDTPNSMVPSPVET",
"mw": 4.031,
"total_mw": 4.031,
"number_molecules": 1,
"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/homeobox protein Lhx4 LIM domains fused to the LIM interaction domain (LID) of Insulin gene enhancer protein ISL-2",
"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": "Philippa",
"contributor_surname": "Stokes",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-11-19",
"storage_temperature": null,
"cell_temperature": 13.5,
"exposure_time": 1.0,
"number_of_frames": 24,
"wavelength": 0.10332,
"sample_detector_distance": null,
"concentration_min": 0.12,
"concentration_max": 1.9,
"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/SASDDQ4_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDQ4_fit1_model1.pdb",
"model_mw": 13.586,
"bead_radius": 2.0,
"log": null,
"symmetry": "None",
"comment": "One of 20 models generated using DAMMIN that went into creating the Damfilt model.",
"user": 205
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDQ4_fit1_model2_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDQ4_fit1_model2.pdb",
"model_mw": 13.381,
"bead_radius": 2.0,
"log": "https://www.sasbdb.org/media/log_files/damselR.log",
"symmetry": null,
"comment": "Damfilt model derived from multiple DAMMIN runs where 20 models were generated, spatially aligned.",
"user": 205
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/DM5RExtr_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 2.715,
"p_value": 0.543254,
"fit_residual_plot": "DM5RExtr_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDQ4_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/DM5RExtr.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The protein analysed consists of a fusion of two interacting partner proteins: the LIM domains of Lhx4 and the LID of Isl2. The ab initio bead models presented in this entry include: 1) The best-fit individual reconstruction (top) and; 2) The spatially aligned and volume/bead occupancy-corrected averaged representation of the protein in solution (bottom) calculated from twenty individual reconstructions (NSD = 0.68; resolution estimate = 2.8 nm). Five concentrations of protein were subjected to SAXS as static samples (96-well plate) at the Australian Synchrotron. Subtle concentration dependent effects were noted. All data and additional information relating to the concentration series is included in the full-entry zip archive. The protein was subjected to SEC (off line) as the last purification step just prior to data collection. Also refer to the related SASBDB entry SASDDR4.",
"experiment_description": "Synchrotron SAXS data from solutions of the LIM domains from LIM/homeobox protein Lhx4 fused to the LIM interaction domain (LID) of Insulin gene enhancer protein ISL-2 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 wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.1 and 1.9 mg/ml were measured at 13.5°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. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 15.0,
"experimental_mw_error": null,
"guinier_i0_mw": 18.0,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.03434,
"pddf_i0_error": 6e-05,
"guinier_i0": 0.034125,
"guinier_i0_error": 0.006,
"pddf_rg": 2.31,
"pddf_rg_error": 0.006,
"guinier_rg": 2.22,
"guinier_rg_error": 0.006,
"pddf_dmax": 8.0,
"pddf_dmax_error": null,
"porod_volume": 20.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 23,
"guinier_point_last": 128,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDQ4_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
