Table 3.
Data Collection and Refinement Statistics for HDAC6 CD1 Mutant–Inhibitor Complexes
| HDAC6 CD1 Mutant Inhibitor |
H82F/F202Y Trichostatin A |
K330L SAHA-BPyne |
K330L 4-iodo-SAHA |
|---|---|---|---|
| Data Collection | |||
| Beamline | APS, 24-ID-C 24-ID-C |
NSLS-II, 17-ID-1 17-ID-1 (AMX) |
APS, 24-ID-E 24-ID-E |
| Wavelength (Å) | 0.98 | 0.92 | 0.98 |
| Temperature (K) | 100 | 100 | 100 |
| Detector | PILATUS 6M-F | Dectris Eiger 9M | Dectris Eiger 16M |
| Wilson B factor (Å2) | 32 | 46 | 15 |
| Crystal-detector distance (mm) | 300 | 230 | 150 |
| Rotation range per image (°) | 0.20 | 0.20 | 0.20 |
| Total rotation range (°) | 180 | 180 | 180 |
| Exposure time per image (s) | 0.20 | 0.02 | 0.20 |
| Space group | P21 | C22121 | P21 |
| a,b,c (Å) | 53.1, 124.0, 55.0 | 66.0, 95.2, 119.7 | 53.1, 123.8, 55.1 |
| α, β, γ (°) | 90.0, 114.4, 90.0 | 90.0, 90.0, 90.0 | 90.0, 113.5, 90.0 |
| Rmergeb | 0.054 (0.418) | 0.190 (0.817) | 0.091 (0.271) |
| Rpimc | 0.052 (0.395) | 0.119 (0.507) | 0.071 (0.231) |
| CC1/2d | 0.996 (0.792) | 0.971 (0.618) | 0.981 (0.829) |
| Redundancy | 3.4 (3.2) | 6.4 (6.7) | 2.4 (2.3) |
| Completeness (%) | 98.7 (98.4) | 100.0 (100.0) | 77.9 (80.6) |
| I/σ | 8.9 (1.9) | 4.8 (2.0) | 5.2 (2.0) |
| Refinement | |||
| Resolution (Å) | 48.34-2.30 (2.38-2.30) | 54.25-2.40 (2.49-2.40) | 39.14-1.90 (1.97-1.90) |
| No. reflections | 28350 (2842) | 15104 (1483) | 39267 (3884) |
| Rwork/Rfreee | 0.170/0.232 (0.210/0.256) | 0.204/0.243 (0.263/0.274) | 0.177/0.223 (0.206/0.270) |
| No. atomsf | |||
| Protein | 5288 | 2688 | 5338 |
| Ligand | 50 | 73 | 46 |
| Solvent | 116 | 47 | 268 |
| Average B factors (Å2) | |||
| Protein | 33 | 47 | 14 |
| Ligand | 29 | 44 | 17 |
| Solvent | 31 | 43 | 18 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.007 | 0.002 | 0.007 |
| Bond angles (°) | 0.9 | 0.6 | 0.8 |
| Ramachandran plotg | |||
| Favored | 95.53 | 96.63 | 96.30 |
| Allowed | 4.47 | 3.37 | 3.70 |
| Outliers | 0.00 | 0.00 | 0.00 |
| PDB codes | 6WYO | 6WYP | 6WYQ |
Values in parentheses refer to the highest-resolution shell indicated.
Rmerge = ∑hkl∑i/Ii,hkl − ⟨I⟩hkl∣/∑hkl∑iIi,hkl, where ⟨I⟩hkl is the average intensity calculated for reflection hkl from replicate measurements.
Rp.i.m.= (∑hkl(1/(N-1))1/2∑i∣Ii,hkl − ⟨I⟩hkl∣)/∑hkl∑i Ii,hkl, where ⟨I⟩hkl is the average intensity calculated for reflection hkl from replicate measurements and N is the number of reflections.
Pearson correlation coefficient between random half-datasets.
Rwork = ∑∣∣Fo∣ − ∣Fc∣∣/∑∣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.
Per asymmetric unit.
Calculated with MolProbity.