Water in macromolecular models: Difference between revisions
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==Water per amino acid== | ==Water per amino acid== | ||
Wlodawer ''et al.'' (2008) explain: | |||
<blockquote> | |||
"It should be noted that the inclusion of a water mol- ecule in the model usually increases the number of refinement parameters by four (three coordinates plus the isotropic B-factor) and subsequently decreases the R-factor, so assigning water to each unidentified sec- tion of density is very tempting, but may not be justi- fied. The presence of water molecules with high B-factors (> 100 A ̊ 2) indicates that the solvent struc- ture was not refined very carefully. A large difference in the values of the B-factors for a solvent molecule and its environment is also very suspicious." | |||
</blockquote> | |||
Wlodawer ''et al.'' suggest that | |||
==See Also== | ==See Also== | ||
Revision as of 02:13, 17 August 2021
In PDB files resulting from X-ray crystallography that do specify water positions, typically only 10-20% of the water that was actually present in the crystal is shown. Protein crystals used for X-ray diffraction are about half water[1], but the majority of the water present is disordered and cannot be resolved. Only tightly bound, stationary water molecules can be experimentally resolved in the electron density map. Similarly, in PDB files resulting from NMR, only tightly bound water can be resolved, and the majority of the water is not represented.
The water content of protein crystals ranges from 27% to 65%, average 43%[2][3] or 51%[1].
PDB entries with too much water (>90%) or too little water (<5%) likely signal serious errors[1]. Wlodawer et al. have provided some examples[1].
Water per amino acidWater per amino acid
Wlodawer et al. (2008) explain:
"It should be noted that the inclusion of a water mol- ecule in the model usually increases the number of refinement parameters by four (three coordinates plus the isotropic B-factor) and subsequently decreases the R-factor, so assigning water to each unidentified sec- tion of density is very tempting, but may not be justi- fied. The presence of water molecules with high B-factors (> 100 A ̊ 2) indicates that the solvent struc- ture was not refined very carefully. A large difference in the values of the B-factors for a solvent molecule and its environment is also very suspicious."
Wlodawer et al. suggest that
See AlsoSee Also
ReferencesReferences
- ↑ 1.0 1.1 1.2 1.3 Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J. 2008 Jan;275(1):1-21. doi: 10.1111/j.1742-4658.2007.06178.x. Epub 2007, Nov 23. PMID:18034855 doi:http://dx.doi.org/10.1111/j.1742-4658.2007.06178.x
- ↑ Matthews BW. Solvent content of protein crystals. J Mol Biol. 1968 Apr 28;33(2):491-7. PMID:5700707 doi:http://dx.doi.org/10.1016/0022-2836(68)90205-2
- ↑ Chruszcz M, Potrzebowski W, Zimmerman MD, Grabowski M, Zheng H, Lasota P, Minor W. Analysis of solvent content and oligomeric states in protein crystals--does symmetry matter? Protein Sci. 2008 Apr;17(4):623-32. doi: 10.1110/ps.073360508. PMID:18359856 doi:http://dx.doi.org/10.1110/ps.073360508