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Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQJ PDB ENTRY 2VQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 18% PEG 10000, 1MM DTT
Crystal Properties Matthews coefficient Solvent content 4.9 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.911 α = 90 b = 137.911 β = 90 c = 69.519 γ = 120
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 CCD 2006-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 60 100 0.15 14.3 7.1 15460
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 3 3.48 100 0.84 2.2 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VQJ 3 20 14460 756 100 0.234 0.233 0.261 0.2399 RANDOM 83.6
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] 4.51 2.25 4.51 -6.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_3_deg 17.237 r_dihedral_angle_4_deg 11.797 r_dihedral_angle_1_deg 5.326 r_angle_refined_deg 1.033 r_scangle_it 0.823 r_mcangle_it 0.552 r_scbond_it 0.486 r_mcbond_it 0.298 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_3_deg 17.237 r_dihedral_angle_4_deg 11.797 r_dihedral_angle_1_deg 5.326 r_angle_refined_deg 1.033 r_scangle_it 0.823 r_mcangle_it 0.552 r_scbond_it 0.486 r_mcbond_it 0.298 r_nbtor_refined 0.297 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.136 r_metal_ion_refined 0.098 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2868 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing