NMR paper Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

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[NMR paper] Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

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NMR processing:

MDD

NMR assignment:

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Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

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Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

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HADDOCK

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NMR model quality:

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Methyl S2

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Shiftx2

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ArShift- Aromatic

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Camcoil

Poulsen_rc_CS

Disordered proteins:

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04-06-2014, 02:01 AM

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Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):958-67

Authors: Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C

Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

PMID: 24699641 [PubMed - in process]

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