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Crystal Structure of Human HDAC8 complexed with MS-344
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T64 PDB ENTRY 1T64
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 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.644 α = 90 b = 80.644 β = 90 c = 105.523 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 2001-05-18 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 2.3 69 94 0.051 0.051 30 5.8 17160 16130 33.3
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 2.3 2.4 93 0.55 0.55 2.4 4 1610
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 (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 1T64 2.31 69.01 17160 16130 869 94.91 0.215 0.21247 0.2074 0.27368 RANDOM 33.35
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] 3.6 1.8 3.6 -5.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.42 r_scangle_it 1.661 r_angle_refined_deg 1.137 r_scbond_it 1.062 r_mcangle_it 0.631 r_mcbond_it 0.337 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.42 r_scangle_it 1.661 r_angle_refined_deg 1.137 r_scbond_it 1.062 r_mcangle_it 0.631 r_mcbond_it 0.337 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.081 r_metal_ion_refined 0.039 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing