Related Experiment Video
Updated: May 27, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures
Joshua SungWoo Yang1, Ji-han Kim, Sangho Oh
1Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-Gu, Daejeon 305-806, The Republic of Korea.
Abstract:
According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. We present a public database of 2405 refined NMR solution structures [statistical torsion angle potentials (STAP) refinement of the NMR database, http://psb.kobic.re.kr/STAP/refinement] from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analysed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, χ(1)-χ(2) rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.
Related Concept Videos
NMR Spectrometers: Resolution and Error Correction
Chemical Shift: Internal References and Solvent Effects
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.

