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The native model was rebuilt in COOT according to 2FOFC and 1FOFC map and refined at 1.60 Å resolution against the wild-type SaTRIC native data with phenix.refine50.refine50
The H atoms of the water molecules in the structure of (1) were located from the difference map and refined with no positional constraints.
To reduce potential model bias during phasing, a polyalanine model was built into the initial map and refined before side chain modelling.
The polar hydrogens were identified from the difference map and refined isotropically, with the exception of H9 in SDMSO, where the position was refined with a constrained O−H bond distance.
b d Dark channel, transmission map, and refined transmission map of (a).
The hydrogen atoms were located from the difference Fourier map and refined isotropically.
Similar(49)
Subsequently, we computed map distances and refined the locus order with other purpose-built perl scripts.
In the pre-processing stage, PHLAT applies a genome-wide reference for Bowtie 2 mapping, and refines the mapped reads using a stringent threshold for mismatches.
Findings from the different streams of evidence were interrogated, discussed, mapped, charted and refined through further discussion within the research team to build a deeper understanding.
A 3D map was generated and refined by projection matching to a resolution of 19 Å as determined by Fourier shell correlation at FSC=0.143 (Rosenthal and Henderson, 2003) (Supplementary Figure S2A).
This interface includes procedures to initially place markers on a map and refine map order, as well as a number of utility routines.
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