Table 3. Summary of the 15 highest peaks observed in a radiation-damage difference map.
The APC5871 crystal was not used in this analysis because the very low multiplicity of observations did not allow zero-dose extrapolation, which is necessary for RDDEM coefficient determination of the map. The VAV protein was excluded, as the final model has not yet been deposited. For the p37n33 structure, determined by sulfur SAD phasing (Dann, unpublished work), PDB entry 3e79 (Sippel et al., 2008 ▶) was used as a reference point. For each protein, all peaks with σ values outside the ±5σ (r.m.s.) range were analyzed. Numbering of solvent molecules follows that of the PDB depositions; however, in the case of the iodide soak, for which only the native structure has been deposited, the water-molecule number is specified to provide the location of the I-atom positions. Superscripts indicate the protein chain, whereas subscripts indicate the type of atom when the RDDEM peak could be assigned to a single atom.
| Protein | APC35880 | NaI-841 | p37n33 | Tp0655 |
|---|---|---|---|---|
| PDB code | 1t0t | 1r61 | 3e79 | 2v84 |
| 1 | MSE73V (−10.86) | H2O2015A and H2O2016A (−8.02) iodide | ThiamineS1 (−13.34) | E150A (−11.24) decarboxylation |
| 2 | MSE73W (−10.74) | H2O2023B and H2O2024B (−6.16) iodide | E146A (−8.89) decarboxylation | MESS 1326 (−9.23) |
| 3 | MSE239X (−10.65) | H2O2025A (−6.09) iodide | E146A (−8.86) decarboxylation | E211A (−7.16) decarboxylation |
| 4 | MSE239V (−10.19) | H2O2061A (−5.58) iodide | E79A (−8.31) decarboxylation | MSD152A (+6.79) position change |
| 5 | MSE73X (−10.13) | H2O2012A (−5.54) iodide | K403A (−8.15) decarboxylation | D147A (−6.41) decarboxylation |
| 6 | MSE73Y (−9.90) | E124A (−5.51) decarboxylation | E393A (−7.94) decarboxylation | D64A (−6.24) decarboxylation |
| 7 | MSE239Z (−9.22) | H2O2014A (−5.25) iodide | E157A (−7.83) decarboxylation | Solvent area (−6.16) |
| 8 | MSE73Z (−9.05) | D141B (−5.20) decarboxylation | NO213A (−7.76) | MSD145A (+6.16) position change |
| 9 | MSE239W (−8.61) | D70A (−5.18) decarboxylation | H2O1035A (−7.72) | MSD145A (−6.10) position change |
| 10 | MSE239Y (−8.22) | Solvent area (4.99) possible iodide | H2O1092A (−7.68) | E263A (−5.94) decarboxylation |
| 11 | D16V (−7.86) decarboxylation | Solvent area (−4.91) possible iodide | ThiamineN4 (−7.67) | GO115A (+5.93) |
| 12 | MSE216V (−7.53) | D70A (−4.91) decarboxylation | E393A (−7.65) decarboxylation | H2O2128A (−5.93) |
| 13 | MSE146V (−7.31) | DN141B (+4.83) | E393A (−7.49) decarboxylation | K305A (−5.86) position change |
| 14 | MSE146W (−7.26) | PCG195A (+4.8) | D388A (−7.48) decarboxylation | E104A (−5.80) decarboxylation |
| 15 | D147Z (−7.18) decarboxylation | MSD181B (−4.74) | D159A (−7.44) decarboxylation | K305A (−5.68) position change |
| No. of peaks† | 57 | 9 | 104 | 29 |
No. of peaks that are either lower than −5σ or higher than 5σ.