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Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.

ABSTRACT: Binder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13-2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent content in the Protein Data Bank.

SUBMITTER: Kolenko P

PROVIDER: S-EPMC10405593 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.

Kolenko Petr P Mikulecký Pavel P Pham Phuong Ngoc PN Malý Martin M Schneider Bohdan B

Journal of applied crystallography 20230616 Pt 4

Binder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13-2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent con ...[more]

PMID: 37555209

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Project description:This study aims to solve the site-occupancy issues of any crystalline substance, showing that the structure refinement results should not be limited to a simple description of the crystal geometry but should go beyond that, providing refined site-scattering values consistent with the chemical data. A detailed description of the structure of the amphibole-supergroup minerals is very challenging owing to their complex chemical composition that renders the process of cation partition extremely difficult, particularly because of the occurrence of multivalent elements. Since amphiboles naturally occur under a fibrous morphology and have largely been used to produce asbestos, there is a growing demand for detailed and accurate structural data in order to study the relationships between structure, composition and toxicity. The present study proposes a recommended refinement procedure for both X-ray single-crystal structure refinement (SREF) and Rietveld analysis for tremolite, selected as a test case. The corresponding structural results are compared to estimate the ‘degree of confidence’ of the Rietveld refinement with regard to SREF. In particular, it is shown that the interpretation of the electron density of the tremolite structure by SREF is model dependent. By assuming that the site-scattering values from SREF should be as close as possible to those from electron microprobe analysis, as a crucial constraint for the correct description of the final crystal-chemical model, it is found that it is best satisfied by using partially ionized scattering curves (SCs) for O and Si, and neutral SCs (neutral oxygen curves or NOCs) for other atoms. This combination leads to the best fit to the diffraction data. Moreover, it is found that Rietveld refinement using NOCs produces the best structural results, in excellent agreement with SREF. It is worth noting that, due to the complexity of the diffraction pattern and the fairly large number of freely refinable parameters, refinements with different combinations of SCs produce results almost indistinguishable from a statistical point of view, albeit showing significant differences from a structural point of view.

Dataset Information

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.

Publications

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.

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