Ccpnmr

Manufactured by Bruker

CcpNmr is a software package developed by Bruker for the analysis and processing of nuclear magnetic resonance (NMR) data. The core function of CcpNmr is to provide a comprehensive suite of tools for the visualization, assignment, and analysis of NMR spectra.

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Lab products found in correlation

Topspin, by Bruker (2 mentions) Cryogenic probe, by Bruker (1 mentions) Avance 3 hd, by Bruker (1 mentions)

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CcpNmr Analysis (5 citations)

2 protocols using ccpnmr

NMR Relaxation Experiments for Xt3a

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¹⁵N spin-lattice (R₁), transverse (R₂) relaxation, and ¹H-¹⁵N NOE experiments for Xt3a were recorded at 25 °C on a 900 MHz spectrometer equipped with cryogenic probe (Bruker, Billerica, MA). The sample contained 500 μM of ¹⁵N/¹³C labeled Xt3a (as above). The relaxation delay was sampled at 10, 20, 60, 100, 200, 400, 600 and 1200 ms for the R₁ experiments and 16, 33, 67, 135, 169, 203, 237 and 271 ms for the R₂ measurements. Spectra were processed using Topspin (v4.1.3, Bruker) and the signal decay was analysed and plotted using CcpNmr (v2.4.1). The time constant error (TC in CcpNmr) from the exponential fit is used in the the R₁ and the R₂ plots. The noise in the spectrum (relative to the peak height) was used to estimate the uncertainty (error bars) in the heteronuclear NOE plots.

Maxwell M.J., Thekkedam C., Lamboley C., Chin Y.K., Crawford T., Smith J.J., Liu J., Jia X., Vetter I., Laver D.R., Launikonis B.S., Dulhunty A., Undheim E.A, & Mobli M. (2023). A bivalent remipede toxin promotes calcium release via ryanodine receptor activation. Nature Communications, 14, 1036.

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NMR Spectroscopy of Labeled Proteins

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NMR spectra were collected on an 800 MHz AVANCE III HD spectrometer (Bruker) with a 5 mM cryoprobe. Proteins were in 90% H₂0/10% D₂0 with 50 mM sodium phosphate and 200 mM sodium chloride (pH 6.8). One dimensional proton spectra were collected using WATERGATE solvent suppression ^{31 (link)}. Two dimensional ¹H,¹⁵N-HSQC were collected on uniformly labeled ¹⁵N samples using the ‘hsqcfpf3gpphwg’ pulse sequence from the Bruker library modified to use excitation sculpting water suppression. Labeled samples were grown as described previously, except that prior to induction, cultures were centrifuged and transferred to a minimal media containing 1.0 g/L of ¹⁵N ammonium chloride. NMR samples had concentrations ≥200 μM, as protein solubility allowed. All spectra were processed and visualized using TopSpin (Bruker) and CCPNMR ^{32 (link)}.

Murphy G.S., Greisman J.B, & Hecht M.H. (2015). De Novo Proteins with Life-Sustaining Functions are Structurally Dynamic. Journal of molecular biology, 428(2 0 0), 399-411.

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