Table 2. Backbone amide (1DNH) RDC analysis of apo and holo Alkbh5.
Used RDCs | No. of RDCs | (Hz)* | η* | Rfac (%)† |
Back-calculation of RDC data from x-ray structure | ||||
Apo—All RDC | 184‡ | 8.5 | 0.30 | 47.9 |
Apo—Best fit | 121 | 15.6 | 0.50 | 20.1 |
Zn2+/αKG—All RDC | 185‡ | 10.4 | 0.32 | 47.7 |
Zn2+/αKG—Best fit | 121 | 15.5 | 0.51 | 19.8 |
Zn2+/αKG/m6A—All RDC | 110‡ | 14.0 | 0.63 | 48.0 |
Zn2+/αKG/m6A—Best fit | 76 | 21.2 | 0.39 | 21.4 |
Ensemble refinement | ||||
Apo—All RDC l | 192‡ | – | – | 25.8 |
Zn2+/αKG—All RDC | 193‡ | – | – | 25.1 |
Zn2+/αKG/m6A—All RDC | 116‡ | – | – | 25.6 |
* and η are the magnitude and rhombicity of the alignment tensor, respectively.
†The RDC Rfac is given by , where Dobs and Dcalc are the observed and calculated RDCs, respectively (57, 58).
‡More RDCs are used in the ensemble refinement than in SVD, as the data from residues that are missing from the x-ray structure could not be used for the SVD fitting.