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Figure 5
Selected examples of (2mFobs − DFmodel, φmodel) nuclear density map improvement after re-refinement of structure 1c57 (neutron data). Left, original structure; right, after re-refinement in phenix.refine. Maps are contoured at the 1.5σ level. Note the improved orientation of exchangeable H/D atoms at Ser and Tyr O atoms. The systematic lack of density around H atoms is a consequence of the negative scattering length of H atoms and related density-cancellation effects (Afonine, Mustyakimov et al., 2010BB11).

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 68| Part 4| April 2012| Pages 352-367
https://doi.org/10.1107/S0907444912001308
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