TABLE 1.
Crystallographic data collection and phasing statistics
| HDAC6 | HDAC + peptide RLRGG | HDAC6 + ubiquitin | |
|---|---|---|---|
| Protein Data Bank code | 3C5K | 3GV4 | 3PHD |
| Space group | P 21 2121 | P 212121 | P43212 |
| Unit cell | a = 40.5 b = 45.1 c = 55.8 | a = 31.7 b = 36.1 c = 89.0 | a = b = 133.7, c = 118.8 |
| Beamline | BNL X29A | RIGAKU FR-E | APS,23ID-B |
| Wavelengtha | 1.26 | 1.54 | 1.03317 |
| Resolution | 50–1.55 | 50–1.72 | 50–3.0 |
| Unique reflections | 10,033 | 10,865 | 22,204 |
| Data redundancy | 10.8 (6.0) | 5.8 (3.1) | 16.2 (16.5) |
| Completeness (%) | 98.0 (80.5) | 94.9 (72.5) | 100 (100) |
| I/σ(I) | 43.7 (5.8) | 28.0 (4.3) | 45.8 (4.7) |
| Rsymb | 0.071 (0.20) | 0.073 (0.23) | 0.091 (0.767) |
| Refinement | |||
| Resolution | 35.07–1.55 | 33.45–1.72 | 32.7–3.0 |
| Reflections used | 9546 | 10,213 | 22,135 |
| All atoms (solvent) | 1000 (156) | 1010 (205) | 3331 (2) |
| Rwork/Rfree (%)c | 17.3/22.7 | 17.4/23.0 | 23.5 (26.5) |
| Root mean square deviation | |||
| Bond length | 0.008 | 0.010 | 0.01 |
| Bond angle | 1.15 | 1.19 | 1.12 |
| Mean B factor | 10.9 | 22.0 | 72.9 |
| Molprobidity Ramachandran plot | |||
| Favored (%) | 97.2 | 96.0 | 93.98 |
| Allowed (%) | 100 | 100 | 99.8 |
| Outliers (%) | 0 | 0 | 1 |
a Apo-structure was collected at peak zinc wavelength.
b Rsym = sum(|I − <I>|)/sum(<I>), where I is the observed intensity, and <I> is the average intensity from multiple observations of symmetry-related reflections.
c Rfree value was calculated with ∼5% of the data.