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Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M BisTris, 18 to 24% PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.53 α = 90 b = 105.53 β = 90 c = 88.86 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9173 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 45.7 98.7 0.14 7.7 4.7 59433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.206 97.2 0.574 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3c0y 2.15 45.7 56390 3018 98.7 0.19447 0.19264 0.1987 0.2284 0.2336 RANDOM 28.716
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.17 0.09 0.17 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 12.844 r_dihedral_angle_1_deg 6.076 r_long_range_B_refined 3.764 r_long_range_B_other 3.731 r_scangle_other 2.224 r_mcangle_it 2.135 r_mcangle_other 2.135 r_scbond_it 1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.364 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 12.844 r_dihedral_angle_1_deg 6.076 r_long_range_B_refined 3.764 r_long_range_B_other 3.731 r_scangle_other 2.224 r_mcangle_it 2.135 r_mcangle_other 2.135 r_scbond_it 1.333 r_scbond_other 1.333 r_angle_refined_deg 1.268 r_mcbond_it 1.252 r_mcbond_other 1.251 r_angle_other_deg 0.954 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7942 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling PHASER phasing