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Crystal structure of human HDAC2 in complex with TNG260
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 35% PEG 600, 100 mM CHES pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.26 45.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.23 α = 90 b = 97.31 β = 90 c = 139.01 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 PILATUS3 6M 2021-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.8 48.66 99 0.101 0.996 9.1 3.6 221686 23.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.849 90.8 0.819 0.561 1.54 2.1
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 1.8 48.66 1.34 221677 3815 98.95 0.1611 0.1604 0.1624 0.1967 0.1969 29.61
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 14.3624 f_angle_d 0.7986 f_chiral_restr 0.0542 f_plane_restr 0.0083 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8879 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 313
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing