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Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W22 PDB ENTRY 1W22 AND A MODEL BUILD FROM A SAD DATASET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.6M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 10% DIOXANE 1MM DTT
Crystal Properties Matthews coefficient Solvent content 2.85 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.77 α = 90 b = 137.562 β = 90 c = 68.993 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 CCD ADSC CCD 2005-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.1 84 100 0.06 31.3 7.2 28496 2
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 2.1 2.14 99.6 0.52 3.12 5.5
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 1W22 AND A MODEL BUILD FROM A SAD DATASET 2.1 84 28496 1516 99.9 0.228 0.225 0.2234 0.276 0.2735 RANDOM 36.84
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] 3.36 -1.62 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 16.313 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_1_deg 6.019 r_scangle_it 2.211 r_scbond_it 1.441 r_angle_refined_deg 1.315 r_mcangle_it 1.175 r_angle_other_deg 0.927 r_mcbond_it 0.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 16.313 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_1_deg 6.019 r_scangle_it 2.211 r_scbond_it 1.441 r_angle_refined_deg 1.315 r_mcangle_it 1.175 r_angle_other_deg 0.927 r_mcbond_it 0.636 r_symmetry_vdw_refined 0.307 r_symmetry_vdw_other 0.235 r_nbd_refined 0.217 r_nbd_other 0.181 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.124 r_nbtor_other 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 3021 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing