Water in macromolecular models

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In PDB files resulting from X-ray crystallography that do specify water positions, only a small fraction of the water that was actually present in the crystal is present in the atomic model. 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]. The water content is given in the PDB file:

REMARK 280 SOLVENT CONTENT, VS   (%): 52.00

and in the mmCIF file:

_exptl_crystal.density_percent_sol   52.0

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 acid

Wlodawer et al. (2008)^[1] explain:

"It should be noted that the inclusion of a water molecule 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 section of density is very tempting, but may not be justified. The presence of water molecules with high B-factors (> 100 A ̊ 2) indicates that the solvent structure 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 in general, the number of water molecules per amino acid should not exceed 3 minus the resolution in Å^[1].

"Thus at low resolution (~ 2.5 A ̊ ) it should be possible to identify in the electron-density maps at most 0.3–0.5 ordered water molecules per protein residue and at very high resolution (1.0 A ̊ ) this may increase to 2 water molecules per residue. Structures exceeding these limits may contain errors."

These authors proceed to give examples of PDB entries with excessive water that should not be trusted, as well as some good resolution PDB entries where it appears that too few waters were modeled^[1].

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 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