Table 1.
Summary of crystal parameters, data collection, and refinement statistics. Values in parentheses are for the highest resolution shell.
| Se-Met AtmS13 | Native AtmS13 | |
|---|---|---|
| Crystal parameters | ||
| Space group | C2 | R32:h |
| Unit-cell parameters (Å, °) | 204.1, 73.0, 58.6 90.0, 103.7, 90.0 |
223.1, 233.1, 460.9 90.0, 90.0, 120.0 |
| Data collection statistics | ||
| Wavelength (Å) | 0.97929 | 0.98000 |
| Resolution range (Å) | 29.4–1.50 | 30.0–3.00 |
| No. of reflections (measured/unique) | 560,589/130,016 | 978,914/95,972 |
| Completeness (%) | 97.8 (82.0) | 100.0 (99.0) |
| Rmerge* | 0.063 (0.392) | 0.138 (0.483) |
| Redundancy | 4.3 (3.1) | 10.2 (9.5) |
| Mean I/sigma (I) | 20.6 (3.7) | 7.6 (1.2) |
| CC1/2 | 0.99 (0.84) | 0.99 (0.51) |
| Refinement and model statistics | ||
| Rcryst§/Rfree¶ | 0.145/0.166 | 0.187/0.220 |
| Ligands RSCCa | 0.98 | 0.87 |
| RMSD bonds (Å) | 0.006 | 0.014 |
| RMSD angles (°) | 1.10 | 1.200 |
| B factor – protein/ligand/solvent (Å2) | 16.8/14.3/35.3 | 109.5/73.2/84.1 |
| No. of protein atoms | 6,271 | 20,446 |
| No. of waters | 1155 | 252 |
| No. of auxiliary molecules in the asymmetric unit | 2 LLP# | 1 PLP |
| Ramachandran plot (%) | ||
| Favorable region | 99.0 | 95.0 |
| Additional allowed region | 1.0 | 4.7 |
| Outliers region | 0.0 | 0.3 |
| PDB | 4ZWV | 4XAU |
*
Rmerge = Σh Σi | Ii (h) – <I(h)>|/ΣhΣi Ii(h), where Ii(h) is the intensity of an individual measurement of the reflection and <I(h)> is the mean intensity of the reflection.
§
Rcryst = Σh ‖Fobs| – |Fcalc‖/Σh |Fobs|, where Fobs and Fcalc are the observed and calculated structure-factor amplitudes, respectively.
¶
Rfree was calculated as Rcryst using 5.0 % of randomly selected unique reflections that were omitted from the structure refinement.
a
RSCC is the real-space correlation to electron density calculated by Phenix
#
LLP is the Lys187 PLP internal aldimine