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Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 100 mM Tris, pH 8.0, 500 mM NDSB-201, 12% PEG3350, 18% isopropanol, cryoprotectant: 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.643 α = 90 b = 53.366 β = 109.47 c = 60.893 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 92 2005-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 29.82 84.5 9735 8238 1 26.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2.7 29.82 1 9735 8238 451 84.5 0.179 0.175 0.1785 0.244 0.2477 RANDOM 24.4
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] -4.18 4.31 -4.7 8.88
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 2.28 c_scbond_it 1.54 c_mcangle_it 1.5 c_mcbond_it 0.93 c_angle_deg 0.7 c_improper_angle_d 0.56 c_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2673 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNX refinement HKL-2000 data reduction SCALEPACK data scaling