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Crystal Structure of human HDAC8 complexed with Trichostatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3R PDB entry 1C3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 277 PEG 8000, calcium acetate, imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.014 α = 90 b = 81.014 β = 90 c = 114.178 γ = 90
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 2001-02-20 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 1.9 81 99.31 0.058 0.058 23.8 4.5 54925 54547 18
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) 1 1.9 1.95 99 0.54 0.544 2.5 3.7 3991
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-Factor (All) R-Factor (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 1C3R 1.9 81.65 54925 54547 2908 99.31 0.174 0.172 0.17197 0.173 0.22087 RANDOM 18.006
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] -0.65 -0.65 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.355 r_scangle_it 2.367 r_scbond_it 1.497 r_angle_refined_deg 1.272 r_mcangle_it 0.864 r_mcbond_it 0.471 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.178 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.355 r_scangle_it 2.367 r_scbond_it 1.497 r_angle_refined_deg 1.272 r_mcangle_it 0.864 r_mcbond_it 0.471 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.178 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.099 r_chiral_restr 0.096 r_gen_planes_other 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5608 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing