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Crystal Structure Analysis of Human HDAC8 complexed with APHA in a new monoclinic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W22 PDB entry 1W22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 298 Final drop concentrations of 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG 6000,
50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.381 α = 90 b = 90.171 β = 94.74 c = 92.267 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 ADSC QUANTUM 4 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.00850 NSLS X12B
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 3.3 32 98.8 0.136 8 3.1 21912 21912 66.9
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) 3.3 3.42 99.5 0.435 3.2 3.1 2212
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1W22 3.3 31.5 21881 20842 828 95.2 0.216 0.216 0.2223 0.26 0.2173 RANDOM 60.1
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] -4.6 -5.59 -3.51 8.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.2 c_mcangle_it 1.82 c_scbond_it 1.33 c_angle_deg 1.3 c_mcbond_it 1.02 c_improper_angle_d 0.89 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 2.2 c_mcangle_it 1.82 c_scbond_it 1.33 c_angle_deg 1.3 c_mcbond_it 1.02 c_improper_angle_d 0.89 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8377 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 52
Software Software Software Name Purpose CBASS data collection AMoRE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling