Data

Lysozyme conformational changes with ionic liquids – FTIR, fluorescence, SAXS and crystallography study

RMIT University, Australia
Calum Drummond (Aggregated by) Connie Darmanin (Aggregated by) Hank Han (Aggregated by) Kate Smith (Aggregated by) Tamar Greaves (Aggregated by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.25439/rmt.12705056.v2&rft.title=Lysozyme conformational changes with ionic liquids – FTIR, fluorescence, SAXS and crystallography study&rft.identifier=https://doi.org/10.25439/rmt.12705056.v2&rft.publisher=RMIT University, Australia&rft.description=SAXS experiments were carried out at the SAXS/WAXS beamline at the Australian Synchrotron, Melbourne, Australia. The setup had an automated well plate system, where each sample and blank solvent was drawn into the same capillary to enable accurate buffer subtraction. Ten successive frames of 1 s exposure were collected for each sample under flow. This system has been designed for weakly-scattering protein samples and reduces protein damage through minimizing X-ray radiation dose per molecule. Lysozyme samples were equilibrated for 1 hour before measurement, and 50 μL of each sample were loaded into the 96-well plate used for the automated sampling setup. The q-range for all the SAXS experiments was 0.006 to 0.53 Å−1. Scatterbrain 2.82 was used for SAXS data processing, and Chromixs, DAMMIN and SREFLEX of the ATSAS software package were used for SAXS data analysis. SAXS patterns are presented as the average of the measurements after careful blank subtraction of the corresponding solvent. The radius of gyration (Rg) for lysozyme was calculated from the Guinier approximation through the ATSAS package. The distance distribution function P(r) and the maximum diameter (Dmax) were also obtained using the ATSAS software. CRYSOL was used to screen different lysozyme crystal structures (PDB ID 1dpw, 1dpx, 1lkr, 1lks, 1uco, 3a8z, 3ru5, 3wul, 3wum, 3wun and 193l), and 1dpw was selected as the closest match to the SAXS patterns. The discrepancies χ2 values of the initial structure with the SAXS patterns were provided, while the best refined models in different ILs were selected based on the χ2 values. &rft.creator=Calum Drummond&rft.creator=Connie Darmanin&rft.creator=Hank Han&rft.creator=Kate Smith&rft.creator=Tamar Greaves&rft.creator=Timothy M. Ryan&rft.date=2023&rft_rights=CC-BY-NC-4.0&rft_subject=SAXS data collection&rft_subject=spectroscopy scanning&rft_subject=Crystallographic data&rft_subject=Biological Physics&rft_subject=Physical Sciences not elsewhere classified&rft_subject=Characterisation of Biological Macromolecules&rft_subject=Crystallography&rft_subject=Proteins and Peptides&rft_subject=Biological physics&rft_subject=Other physical sciences not elsewhere classified&rft_subject=Characterisation of biological macromolecules&rft_subject=Proteins and peptides&rft.type=dataset&rft.language=English Access the data

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SAXS experiments were carried out at the SAXS/WAXS beamline at the Australian Synchrotron, Melbourne, Australia. The setup had an automated well plate system, where each sample and blank solvent was drawn into the same capillary to enable accurate buffer subtraction. Ten successive frames of 1 s exposure were collected for each sample under flow. This system has been designed for weakly-scattering protein samples and reduces protein damage through minimizing X-ray radiation dose per molecule. Lysozyme samples were equilibrated for 1 hour before measurement, and 50 μL of each sample were loaded into the 96-well plate used for the automated sampling setup. The q-range for all the SAXS experiments was 0.006 to 0.53 Å−1. Scatterbrain 2.82 was used for SAXS data processing, and Chromixs, DAMMIN and SREFLEX of the ATSAS software package were used for SAXS data analysis. SAXS patterns are presented as the average of the measurements after careful blank subtraction of the corresponding solvent. The radius of gyration (Rg) for lysozyme was calculated from the Guinier approximation through the ATSAS package. The distance distribution function P(r) and the maximum diameter (Dmax) were also obtained using the ATSAS software. CRYSOL was used to screen different lysozyme crystal structures (PDB ID 1dpw, 1dpx, 1lkr, 1lks, 1uco, 3a8z, 3ru5, 3wul, 3wum, 3wun and 193l), and 1dpw was selected as the closest match to the SAXS patterns. The discrepancies χ2 values of the initial structure with the SAXS patterns were provided, while the best refined models in different ILs were selected based on the χ2 values.

Issued: 2020-10-04

Created: 2021-02-05

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