Dataset Information

A community resource of experimental data for NMR / X-ray crystal structure pairs.

ABSTRACT: We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.

SUBMITTER: Everett JK

PROVIDER: S-EPMC4815321 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A community resource of experimental data for NMR / X-ray crystal structure pairs.

Everett John K JK Tejero Roberto R Murthy Sarath B K SB Acton Thomas B TB Aramini James M JM Baran Michael C MC Benach Jordi J Cort John R JR Eletsky Alexander A Forouhar Farhad F Guan Rongjin R Kuzin Alexandre P AP Lee Hsiau-Wei HW Liu Gaohua G Mani Rajeswari R Mao Binchen B Mills Jeffrey L JL Montelione Alexander F AF Pederson Kari K Powers Robert R Ramelot Theresa T Rossi Paolo P Seetharaman Jayaraman J Snyder David D Swapna G V T GV Vorobiev Sergey M SM Wu Yibing Y Xiao Rong R Yang Yunhuang Y Arrowsmith Cheryl H CH Hunt John F JF Kennedy Michael A MA Prestegard James H JH Szyperski Thomas T Tong Liang L Montelione Gaetano T GT

Protein science : a publication of the Protein Society 20150922 1

We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of ta ...[more]

PMID: 26293815

Similar Datasets

Project description:X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so 'sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ?200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.

Dataset Information

A community resource of experimental data for NMR / X-ray crystal structure pairs.

Publications

A community resource of experimental data for NMR / X-ray crystal structure pairs.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure