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Crystal structure of Danio rerio HDAC6 CD1 in complex with trichostatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 23% PEG 3350, 0.2M MGCL2, 0.1M HEPES PH 7.0, SB ADDITIVE A7
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.47 α = 90 b = 93.01 β = 90 c = 118.47 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 PIXEL DECTRIS PILATUS 2M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.5 50 98.1 0.04 20.6 5.5 51661 -3 24.62
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 1.5 1.54 91.8 1.22 1.3 5
Refinement Statistics Diffraction ID Structure Solution 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 HOMOLOGY MODEL 1.499 46.505 1.34 59655 2983 98.13 0.1404 0.1389 0.1422 0.1696 0.1725 30.5
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 14.024 f_angle_d 0.791 f_chiral_restr 0.075 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2794 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing