NMR-guided refinement of crystal structures using 15N chemical shift tensors

被引:0
作者
Toomey, Ryan [1 ]
Wang, Luther [1 ]
Heider, Emily C. [2 ]
Hartman, Joshua D. [3 ]
Nichols, Alexander J. [4 ]
Myles, Dean A. A. [5 ]
Gardberg, Anna S. [5 ]
McIntyre, Garry J. [6 ]
Zeller, Matthias [7 ]
Mehta, Manish A. [4 ]
Harper, James K. [1 ]
机构
[1] Brigham Young Univ, Dept Chem & Biochem, Provo, UT 84602 USA
[2] Utah Valley Univ, Dept Chem, Orem, UT 84058 USA
[3] Univ Calif Riverside, Dept Chem, Riverside, CA 92521 USA
[4] Oberlin Coll & Conservatory, Dept Chem & Biochem, Oberlin, OH 44074 USA
[5] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA
[6] Australian Nucl Sci & Technol Org, Lucas Heights, NSW 2234, Australia
[7] Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA
基金
美国国家科学基金会;
关键词
DENSITY-FUNCTIONAL THEORY; SINGLE-CRYSTAL; PROTEIN; DIFFRACTION; VALIDATION; PEPTIDES;
D O I
10.1039/d4ce00237g
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
An NMR-guided procedure for refining crystal structures has recently been introduced and shown to produce unusually high resolution structures. Herein, this procedure, is modified to include N-15 shift tensors instead of the C-13 values employed previously. This refinement involves six benchmark structures and 45 N-15 tensors. All refined structures show a statistically significant improvement in NMR fit over energy based refinements. Metrics other than NMR agreement indicate that NMR refinement does not introduce errors with no significant changes observed in atom positions or diffraction patterns. However, refinement does change bond lengths by more than experimental uncertainty with most bond types become shorter than diffraction values. Although this decrease is small (1-4 pm), it significantly alters computed N-15 tensors. The NMR refinement was further evaluated by refining two tripeptides. These structures rapidly converged and achieved an NMR agreement equivalent to benchmark values. To ensure accurate comparisons, a complete atomic structure of the tripeptide AGG was determined by single crystal neutron diffraction at 0.58 & Aring; resolution, allowing unambiguous determination of all hydrogen positions. To verify that all NMR refinements represent genuine improvements rather than artifacts of DFT methods, an independent approach was included to evaluate the final NMR refined coordinates. This analysis employs cluster methods and the PBE0 functional. The unusually small N-15 NMR root-mean-square error of the final refined structures (3.6 ppm) supports the conclusion that the changes made represent improvements over both diffraction coordinates and lattice-including DFT energy refined coordinates.
引用
收藏
页码:3289 / 3302
页数:15
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