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. 2010 Jun 4;1(5):453–458. doi: 10.1007/s13238-010-0045-7

Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods

Jing Su 1,✉, Yang Li 1, Neil Shaw 1, Weihong Zhou 2, Min Zhang 3, Hao Xu 4, Bi-Cheng Wang 4, Zhi-Jie Liu 1,✉
PMCID: PMC4875130  PMID: 21203960

Abstract

Sometimes crystals cannot diffract X-rays beyond 3.0 Å resolution due to the intrinsic flexibility associated with the protein. Low resolution diffraction data not only pose a challenge to structure determination, but also hamper interpretation of mechanistic details. Crystals of a 25.6 kDa non-Pfam, hypothetical protein, PF2046, diffracted X-rays to 3.38 Å resolution. A combination of Se-Met derived heavy atom positions with multiple cycles of B-factor sharpening, multi-crystal averaging, restrained refinement followed by manual inspection of electron density and model building resulted in a final model with a R value of 23.5 (Rfree= 24.7). The asymmetric unit was large and consisted of six molecules arranged as a homodimer of trimers. Analysis of the structure revealed the presence of a RNA binding domain suggesting a role for PF2046 in the processing of nucleic acids.

Keywords: low resolution diffraction, PF2046, Bfactor sharpening, a homodimer of trimers

Footnotes

These authors contributed equally to this work.

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