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HDAC1-MTA1 in complex with TICA (5-(Thiophen-2-yl)Isoxazole-3-Carboxylic Acid), the hydrolysis product of WNA1 by HDAC1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Na HEPES (pH 7.5), 1.8 M ammonium sulfate, and 5% PEG400
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.921 α = 90 b = 107.921 β = 90 c = 133.497 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2017-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 40.18 98.7 0.952 7.6 4.2 39904
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.507
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 2.3 40.18 1.34 39844 1940 98.54 0.1724 0.1698 0.1721 0.2242 0.2258 38.73
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 22.5724 f_angle_d 0.8676 f_chiral_restr 0.0501 f_plane_restr 0.0093 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4355 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction Aimless data scaling