For the zCD1-TSA complex, the zCD2-TSA complex, and the zCD2-SAHA complex, X-ray diffraction data were recorded at the Stanford Synchrotron Radiation Lightsource (SSRL), beamline 14-1 (λ = 1.28184 Å). For the MBP-hCD2-TSA complex, unliganded zCD2, the H574A zCD2-substrate 8 complex, and the zCD2-Belinostat complex, X-ray diffraction data were recorded at the Advanced Photon Source (APS), beamline NE-CAT 24-ID-E (λ = 0.97918 Å). For all other structures, X-ray diffraction data were recorded at the Advanced Light Source (ALS), beamline 4.2.2 (λ = 1.00003 Å). Data reduction and integration for all datasets was achieved with HKL2000;50 data collection and reduction statistics are recorded in Supplementary Tables 2–4 . Although Rmerge values were relatively high for some datasets, analysis of CC1/2 values indicated that these datasets were of sufficient quality for satisfactory structure determination and refinement.
All structures were solved by molecular replacement using the program Phaser.51 (link) For the structure of the zCD2–SAHA complex, a model of the HDAC4 catalytic domain in a closed-loop conformation (PDB entry 4CBT)52 (link) was used as the search probe for rotation and translation function calculations. For all other zCD1 and zCD2 structures, the structure of the zCD2-SAHA complex less inhibitor and water molecules was used as a search probe. For the structure determination of the fusion protein MBP-hCD2–TSA complex, maltose binding protein (PDB entry 4EDQ) and the zCD2–TSA complex less ligands and solvent molecules were used as search probes. The graphics program Coot was used for model building53 (link) and Phenix was used for crystallographic refinement.54 (link) Refinement statistics for each final model are recorded inSupplementary Tables 2–4 . The quality of each model was verified with PROCHECK55 and MolProbity.56 (link) Figures were prepared with Pymol and UCSF Chimera.57 (link) The Ramachandran statistics for each model are as follows: zCD1-TSA complex: 90.3% allowed, 9.4% additionally allowed; zCD2-TSA complex: 91.6% allowed, 7.8% additionally allowed; MBP-hCD2-TSA complex: 88.5% allowed, 10.8% additionally allowed; unliganded zCD2: 91.1% allowed, 8.6% additionally allowed; H574A zCD2-substrate 8 complex: 92.2% allowed, 7.3% additionally allowed; Y785F zCD2-substrate 1 complex: 90.6% allowed, 8.7% additionally allowed; Y785F zCD2-substrate 1 complex: 90.6% allowed, 8.7% additionally allowed; zCD2-HC toxin complex: 90.6% allowed, 8.8% additionally allowed; zCD2-trifluoroketone inhibitor complex: 90.5% allowed, 9.0% additionally allowed; zCD2-acetate complex: 90.4% allowed, 9.1% additionally allowed; zCD2-SAHA complex: 91.4% allowed, 8.0% additionally allowed; zCD2-Belinostat complex: 91.1% allowed, 8.5% additionally allowed; zCD2-HPOB complex: 91.0% allowed, 8.7% additionally allowed; zCD2-Panobinostat complex: 89.9% allowed, 9.6% additionally allowed; zCD2-Oxamflatin complex: 89.3% allowed, 10.0% additionally allowed. No backbone torsion angles adopt disallowed conformations in any structure.
All structures were solved by molecular replacement using the program Phaser.51 (link) For the structure of the zCD2–SAHA complex, a model of the HDAC4 catalytic domain in a closed-loop conformation (PDB entry 4CBT)52 (link) was used as the search probe for rotation and translation function calculations. For all other zCD1 and zCD2 structures, the structure of the zCD2-SAHA complex less inhibitor and water molecules was used as a search probe. For the structure determination of the fusion protein MBP-hCD2–TSA complex, maltose binding protein (PDB entry 4EDQ) and the zCD2–TSA complex less ligands and solvent molecules were used as search probes. The graphics program Coot was used for model building53 (link) and Phenix was used for crystallographic refinement.54 (link) Refinement statistics for each final model are recorded in
