☰ Navigation Tabs
Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor
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 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 = 85.605 α = 90 b = 70.673 β = 108.08 c = 88.201 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 2006-09-20 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 1.9 60 99.9 0.1 11.8 3.8 20692
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 1.9 1.95 99.9 0.47 1.6 3.8
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 1.9 60 75011 3935 99.9 0.196 0.194 0.1972 0.221 0.22 RANDOM 16.33
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] 0.63 1.45 -0.4 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_4_deg 15.744 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 5.701 r_scangle_it 2.23 r_scbond_it 1.351 r_angle_refined_deg 1.24 r_mcangle_it 0.961 r_angle_other_deg 0.946 r_mcbond_it 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_4_deg 15.744 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 5.701 r_scangle_it 2.23 r_scbond_it 1.351 r_angle_refined_deg 1.24 r_mcangle_it 0.961 r_angle_other_deg 0.946 r_mcbond_it 0.52 r_symmetry_vdw_other 0.289 r_xyhbond_nbd_refined 0.26 r_nbd_refined 0.221 r_nbd_other 0.182 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.122 r_symmetry_hbond_refined 0.086 r_nbtor_other 0.083 r_chiral_restr 0.07 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 5410 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing