Table 1.
X-ray diffraction data collection and structure refinement statistics
| PDB - construct - global conf. | 5YF5 - WT - ‘closed’ | 5YF6 - C-682 - ‘closed’ | 5YF7 - C-672 - ‘closed’ | 5YF8 - C-672_AA - ‘open’ |
|---|---|---|---|---|
| Data collection a | ||||
| Space group | P 43 21 2 | P 43 21 2 | P 43 21 2 | I 41 2 2 |
| Cell dimensions | ||||
| a, b, c (Å) | 160.0, 160.0, 55.2 | 161.4, 161.4, 56.0 | 162.2, 162.2, 56.8 | 115.8, 115.8, 393.9 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Resolution (Å)b | 60.0–2.50 (2.59–2.50) | 50.0–2.10 (2.18–2.10) | 50.0–2.27 (2.35–2.27) | 60.0–3.40 (3.52–3.40) |
| No. unique reflections | 25 700 | 43 794 | 35 366 | 18 873 |
| R merge | 0.080 (0.52) | 0.066 (0.46) | 0.075 (0.49) | 0.128 (0.52) |
| R meas | 0.087 (0.56) | 0.070 (0.48) | 0.078 (0.51) | 0.142 (0.58) |
| I / σI | 22.0 (4.1) | 34.3 (6.0) | 34.3 (4.5) | 11.7 (3.2) |
| Completeness (%) | 99.7 (100.0) | 100.0 (100.0) | 99.2 (98.3) | 98.8 (99.5) |
| Redundancy | 6.7 (6.8) | 10.3 (10.3) | 12.7 (12.4) | 5.3 (5.1) |
| Structure refinement | ||||
| Resolution (Å) | 2.50 | 2.10 | 2.27 | 3.40 |
| No. unique reflections | 25 631 | 43 679 | 35 259 | 18 708 |
| R work / Rfreec (%) | 18.5 / 24.2 | 18.0 / 22.7 | 19.9 / 24.5 | 23.0 / 27.1 |
| No. atoms | ||||
| Protein | 5 016 | 5 108 | 5 124 | 4 839 |
| Ligand/Ion/Water | / / 81 | / / 344 | / / 211 | 28 / / 9 |
| B-factors (Å2) | ||||
| Protein | 52.4 | 40.2 | 52.4 | 71.3 |
| Ligand/Ion/water | / / 45.4 | / / 41.6 | / / 47.6 | 69.5 / / 63.4 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.008 | 0.007 | 0.007 | 0.010 |
| Bond angles (°) | 0.918 | 0.800 | 0.826 | 1.164 |
| Ramachandran stat.d | 91.1 / 8.5 / 0.2 / 0.2 | 91.9 / 7.9 / 0.2 / 0.0 | 91.1 / 8.6 / 0.3 / 0.0 | 82.6 / 16.1 / 0.9 / 0.4 |
aOne crystal was used for data collection for each structure.
bValues in parentheses are for the highest-resolution shell.
c5% of data are taken for the Rfree set, and the same Rfree set is applied for the WT, C-682 and C-672 structures.
dValues are in percentage and are for most favored, additionally allowed, generously allowed, and disallowed regions in Ramachandran plots, respectively.