Real-space refinement

Hanson JC, Schoenbom BP (1981) Real space refinement of neutron diffraction data from sperm whale carbonmonoxymyoglobin. J Mol Biol 153 117-146... 

Atomic coordinates of atoms in the model of a protein structure can bo refined to more precise values that give a better fit to the experimental data. The so-called real-space refinement procedure optimizes the fit... 

Diamond, R. A real-space refinement procedure for proteins. Acta Cryst. A27. 436-452 (1971). 

Diamond, R. Real-space refinement of the structure of hen egg-white lysozyme J. Molec. Btol. 82, 371-391 (1974). 

REAL SPACE REFINEMENT DIFFERENCE FOURIER SYNTHESES... 

Results from an early unrefined met myoglobin neutron analysis ( ) based on the x ray structure by Watson and Kendrew ( ) showed a total of 106 water peaks. In that analysis, only peaks that had a peak height equivalent to one-half D2O molecule were considered. More recently, Takano (O, in a refined high resolution x-ray analysis of met myoglobin, found 72 water molecules, and in the present refined neutron analysis of CO-Mb, only AO water molecules were found. These water molecules were identified in a difference map where the features depicting the protein had been subtracted. The protein structure itself had been refined by successive real-space refinement of eight... 

The beta version of the warpNtrace procedure in ARP/wARP version 5 was then employed to improve the quality of the maps (53, 54). This procedure alternates between ARP, real space evaluation of atoms including the addition and removal of atoms and real space refinement, and reciprocal space refinement using the CCP4 program Refinac (55). After every tentii cycle, the resulting map is auto-traced, and the auto-traced structure is then subjected to additional cycles of the ARP / Refinac refinement. 

This methodology has also been used to carry out a potential energy-constrained real-space refinement of the structure of BPTI, using limited diffraction data [39]. Figure 6 illustrates how the energy-refined map on the right identifies more of the electron density of Arg-42 than the map on the left. 

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