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Crystal Structure of human HDAC8 complexed with SAHA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T67 pdb entry 1T67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 277 PEG 8000, HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.761 α = 90 b = 80.761 β = 90 c = 105.615 γ = 120
Symmetry Space Group P 31 2 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 ADSC QUANTUM 4 mirrors 2001-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.9 70 95 0.076 0.076 17 5.3 8595 8164 68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 96.5 0.54 0.54 4 5 870
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1T67 2.91 70.71 8595 8164 406 94.14 0.24926 0.2309 0.31027 RANDOM 68.095
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] 2.75 1.38 2.75 -4.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.099 r_scangle_it 1.736 r_angle_refined_deg 1.281 r_scbond_it 1.014 r_mcangle_it 0.836 r_symmetry_hbond_refined 0.458 r_mcbond_it 0.439 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.099 r_scangle_it 1.736 r_angle_refined_deg 1.281 r_scbond_it 1.014 r_mcangle_it 0.836 r_symmetry_hbond_refined 0.458 r_mcbond_it 0.439 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.085 r_metal_ion_refined 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2737 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction