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Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor
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 6.5 0.1M MES PH 6.5, 1.6M AMMONIUM SULPHATE, 10% DIOXANE 1MM DTT
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.524 α = 90 b = 70.766 β = 108.57 c = 89.011 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 CCD 2007-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 30 98.2 0.18 6.7 2.9 12577
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 3.48 99.5 0.45 2 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VQJ 3.3 30 12576 650 98.2 0.235 0.234 0.2318 0.265 0.2692 RANDOM 31.45
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] 4.15 1.94 -4.1 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 18.587 r_dihedral_angle_3_deg 16.559 r_dihedral_angle_1_deg 5.861 r_scangle_it 1.328 r_angle_refined_deg 1.087 r_angle_other_deg 0.852 r_scbond_it 0.745 r_mcangle_it 0.609 r_mcbond_it 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 18.587 r_dihedral_angle_3_deg 16.559 r_dihedral_angle_1_deg 5.861 r_scangle_it 1.328 r_angle_refined_deg 1.087 r_angle_other_deg 0.852 r_scbond_it 0.745 r_mcangle_it 0.609 r_mcbond_it 0.318 r_symmetry_vdw_other 0.242 r_nbd_refined 0.227 r_nbd_other 0.18 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.085 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 5323 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing