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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Givinostat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/ml HDAC6 CD1
2 mM Inhibitor
0.2 M magnesium formate dihydrate
20% PEG 3350
1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.53 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.16 α = 90 b = 60.4 β = 90 c = 122.16 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2019-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
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 1.4 42.9476472842 99.7 0.094 0.04 0.995 12.4 6.5 80865 11.016022672
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 1.4 1.45 99.7 0.359 0.15 0.952 5.6 6.7
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 5EEF 1.40000794136 42.9476472842 1.33792355939 80865 4046 99.6917955988 0.152590456209 0.151739496756 0.1521 0.16849740174 0.1696 15.2124829674
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 20.9435509501 f_angle_d 0.841288367647 f_chiral_restr 0.077647729394 f_bond_d 0.00584185692849 f_plane_restr 0.00583739087982
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2756 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing