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![[Figure 3]](qe5005fig3mag.jpg)
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Figure 3
Comparison between the traditional representation of partially 1H/2H-exchanged structures and perdeuterated structures and the deuterium fraction representation in mmCIF files. (a) Traditional exchangeable 1H/2H sites representation extracted from the mmCIF file of PDB entry 1vcx. The 1H atom bonded to the main-chain N atom of Ile40 is partially exchanged with 2H. 1H and 2H isotopes have separate atom rows in the atom table with alternative locations A and B (green). The sum of their total occupancy (green) is set to 1.0 (the occupancy values of the 1H and 2H atoms are 0.07 and 0.93, respectively). The H atoms bonded to CA and CB of Ile40 are not exchanged during the partial deuteration procedure; their occupancy value is equal to 1.0. (b) Deuterium fraction representation created by REFMAC5. A new column has been created that specifies the fraction of the deuterium substitution (where 100% is fully deuterated) for the exchanged H atoms. 2H atoms are not present in the atom table, only 1H atoms with the corresponding deuterium fraction parameters (red). The 1H atom bonded to the main-chain N atom of Ile40 has a deuterium fraction value of 0.92, while the 1H atoms bonded to CA and CB of Ile40 are not exchanged, hence the deuterium fraction for these H atoms is zero. (c) Traditional perdeuterated sites representation extracted from the mmCIF file of PDB entry 3rz6. Here, all of the H atoms of Ile7 have been substituted with 2H atoms. There are no 1H atoms in the traditional perdeuterated structures. The occupancy of the 2H atoms is set to 1.0 by convention. (d) Deuterium fraction representation for perdeuterated structures. All 2H atoms are converted to 1H atoms, the corresponding deuterium fractions are refined and values close to 1.0 are obtained. |
![[Figure 3]](qe5005fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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