Table 1.
Crystallographic refinement statistics and model geometry.
| Model | 3P9D + 3P9E (Dekker et al.) | XL-MS (Refmac, NCS, no TLS) | XL-MS (Refmac, NCS, TLS) |
|---|---|---|---|
| resolution limits | 30 – 3.8 | 30 – 3.8 | 30 – 3.8 |
| Rwork / Rfree | 0.3178 / 0.3513 | 0.2696 / 0.3279 | 0.2568 / 0.3046 |
| Figure of merit | 0.672 | 0.715 | 0.751 |
| number of atoms | |||
| Protein | 110444 | 119056 | 119056 |
| Ligand/ion | 784 | 1024 | 1024 |
| Water | 7 | 0 | 0 |
| average B factors | |||
| Protein (Å2) | 141 | 125 | 139 |
| Ligand / ion (Å2) | 130 | 103 | 123 |
| Water (Å2) | 43 | - | - |
| r.m.s. deviations | |||
| bonds (Å) | 0.012 | 0.007 | 0.007 |
| angles (°) | 0.986 | 1.052 | 1.068 |
| Ramachandran plot | |||
| % preferred (Coot) | 85.8 % | 89.5 % | 90.1 % |
| % outliers (Coot) | 4.68 % | 3.16% | 2.89 % |
| number non-Proline cis peptides | 184 | 0 | 0 |
In order to allow a fair comparison with the original model (Dekker; PDB codes 3P9E/3P9D), the XL-MS model was also refined without TLS B-factor parameterization (middle column). The statistics for the Dekker model were determined using Refmac using the default values from CCP4i.