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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NR160
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/mL zCD2 protein, 2 mM NR160 inhibitor, 0.2 M ammonium citrate tribasic, pH 7.0, 20% w/v PEG3350, 1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55 α = 90 b = 83.13 β = 98.33 c = 88.59 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 PIXEL DECTRIS PILATUS 6M-F 2019-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.48 60.32 97.2 0.08 0.052 0.996 9.3 3.2 127210 10.944557782
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.53 95.7 0.57 0.402 0.646 2.8
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 5EEM 1.48000295888 60.3180111193 1.33645495478 127210 6325 96.9773203735 0.16521452676 0.164316413885 0.1649 0.182431534659 0.1829 16.1458348663
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 10.0212053254 f_angle_d 0.840262528347 f_chiral_restr 0.0796121267776 f_plane_restr 0.00588794405191 f_bond_d 0.00569741692261
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5525 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing