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Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with inhibitor Mz327
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 286 0.1 M bis-Tris (pH 6.0), 0.2 M KSCN, 20% PEG 3350 (w/v), 3% (v/v) ethanol
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.244 α = 73 b = 55.544 β = 89.9 c = 74.399 γ = 82.82
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 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.766 29.05 96.1 0.131 0.121 0.986 5.4 2.7 69137 13.91
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 1.776 1.81 89.2 0.552 0.352 0.649 1.5 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.766 29.047 1.96 69115 2000 96.19 0.1942 0.1932 0.193 0.2305 0.2305
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 10.475 f_angle_d 1.028 f_chiral_restr 0.063 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5489 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing