Table 2.
Crystallographic data collection and refinement statistics
| HDAC8 mutant | G302A | G303A | G304A | G305A |
|---|---|---|---|---|
|
Unit Cell
| ||||
| Space group | P21 | P21 | P21 | P21 |
| a, b, c (Å) | 53.1, 84.5, 94.6 | 97.7, 83.8, 99.8 | 53.5, 83.9, 98.4 | 53.0, 82.9, 94.6 |
| α,β, γ (°) | 90.0, 99.0, 90.0 | 90.0, 91.7, 90.0 | 90.0, 101.8, 90.0 | 90, 99.1, 90 |
|
Data Collection | ||||
| Wavelength (Å) | 0.97919 | 0.97923 | 1.18076 | 0.97923 |
| Resolution (Å) | 52.52–1.90 | 97.66–2.41 | 52.36–1.95 | 82.95–1.87 |
| Total/unique no. of reflections | 469621/65162 | 219182/62588 | 189166/62024 | 238947/65132 |
| Rmerge a,b | 0.141 (0.951) | 0.068 (0.313) | 0.078 (0.473) | 0.045 (0.306) |
| CC(1/2)a,c | 0.995 (0.745) | 0.996 (0.836) | 0.991 (0.785) | 0.998 (0.867) |
| I/σ (I)a | 9.8 (2.7) | 12.5 (3.5) | 8.0 (2.5) | 15.4 (3.5) |
| Redundancya | 7.3 (7.3) | 3.5 (2.9) | 3.0 (3.0) | 3.7 (3.1) |
| Completeness (%)a | 100 (100) | 99.9 (99.4) | 99.8 (100) | 97.2 (93.7) |
|
Refinement | ||||
| No. of reflections used in refinement/test set | 65134/3260 | 62558/2928 | 61982/3219 | 65094/6273 |
| Rworka,d | 0.176 (0.244) | 0.180 (0.223) | 0.175 (0.224) | 0.172 (0.231) |
| Rfreea,d | 0.208 (0.308) | 0.212 (0.281) | 0.200 (0.258) | 0.210 (0.283) |
| No. of nonhydrogen atoms: | ||||
| protein | 5649 | 11050 | 5534 | 5549 |
| ligand | 102 | 208 | 63 | 154 |
| solvent | 303 | 211 | 391 | 349 |
|
Average B-factors (Å2) |
||||
| protein | 23 | 26 | 29 | 29 |
| ligand | 30 | 37 | 40 | 35 |
| solvent | 28 | 24 | 34 | 34 |
|
Root-mean-square deviation from ideal geometry |
||||
| bonds (Å) | 0.007 | 0.003 | 0.006 | 0.006 |
| angles (°) | 0.84 | 0.51 | 0.80 | 0.74 |
| Ramachandran plot (%)e | ||||
| favored | 97.0 | 97.0 | 98.4 | 98.9 |
| allowed | 2.9 | 2.9 | 1.6 | 1.1 |
| generously allowed | 0.1 | 0.1 | 0.0 | 0.0 |
|
| ||||
| PDB accession code | 5THS | 5THT | 5THU | 5THV |
a
Values in parentheses refer to the data from the highest shell.
b
Rmerge = Σ|Ih − 〈I〉hI|/ΣIh, where 〈I〉h is the average intensity calculated for reflection h from replicate measurements.
c
Pearson correlation coefficient between random half-datasets.
d
Rwork = Σ||Fo| − |Fc||/Σ|Fo| for reflections contained in the working set. |Fo| and |Fc| are the observed and calculated structure factor amplitudes, respectively. Rfree is calculated using the same expression for reflections contained in the test set held aside during refinement.
e
Calculated with PROCHECK.31