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Structure of the histone deacetylase Clr3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQW 2VQW (HDAC4)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 20% Ethyleneglycol
10% PEG 8000
0.1M MOPS/HEPES
0.04M Sodium nitrate
0.04M Sodium monophosphate
0.04M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.487 α = 90 b = 187.259 β = 90 c = 142.633 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97924 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.4 46.815 98.9 0.072 1 14.86 6.6 31830 52.3
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) 1 2.4 2.46 87.7 0.6 2.5 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VQW (HDAC4) 2.4 46.815 1.36 31826 1524 98.95 0.1888 0.1868 0.1929 0.2279 0.2298
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.392 f_angle_d 0.646 f_chiral_restr 0.028 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4705 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing