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Subsequent model refinement and addition of ordered solvent was carried out using the autobuild and refinement modules of Phenix with manual rebuilding in Coot, which was also used to introduce the sequence changes into the model (T172R, G173Q, L196C, and I301C).
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As such, this construct should not be considered complete, but rather "fit-for-purpose" and suitable for continued refinement, expansion, and addition of influential components of interest (e.g., sclerostin, Wnt pathway, vitamin D kinetics and direct actions, metalloproteinases, etc).
A clutch of gameplay refinements and additions – right-stick camera control being the most instantly appealing of them – ensure that LOS2 improves on the original, while a 20-something-hour campaign promises explorative depth and fan-pleasing visual cues harking back to previous titles.
We believe these refinements and additions will further increase the availability of digitized data and enhance the opportunities for specimen-based botanical research.
Manual model rebuilding was done with Coot [62], and structure refinement and the addition of waters was done with CNS [63].
The coding frame will be revised to allow for refinement of and additions to the principles and standards as new codes are developed inductively from the data.
After refinement of side chains and addition of solvent molecules, difference electron density was present for part of the PSR-3-283A PSR-3-283A PSR-3-283Ae actinhibitor
Intron-exon boundary refinements and UTR additions were performed by annotators viewing alignments generated by the Eukaryotic Genome Control (EGC) computational pipeline (see methods) using the Annotation Station graphical user interface.
The effect of modification and refinement with Sb addition is more effective than that with Ca addition.
Protein structures were prepared using the protein preparation wizard of maestro 9.3 [58], following the default protocol which accounts for energy refinement, hydrogen addition, pKa assignment, and side-chain rotational isomer refinement.
For each refinement, in addition to calculating the FSC between the refined model and the map it was refined against (the FSCwork, red curves in Figure S3), we also calculated a cross-validated FSC between the refined model and the other half map (the FSCtest curve green in Figure S3).
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