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Structure of Human HDAC2 in complex with inhibitor N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600)
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.136 α = 90 b = 98.48 β = 90 c = 139.203 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 CCD ADSC QUANTUM 315r 2018-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.62 50 99.3 0.071 0.083 0.042 0.997 10.1 3.7 159457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.71 99.8 0.595 0.697 0.359 0.768 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LY1 1.62 50 151159 8173 99.06 0.16523 0.16352 0.1651 0.19636 0.1971 RANDOM 27.329
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] -0.94 1.78 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.334 r_dihedral_angle_4_deg 23.568 r_dihedral_angle_3_deg 13.695 r_long_range_B_refined 7.923 r_dihedral_angle_1_deg 5.823 r_scbond_it 4.298 r_mcangle_it 3.273 r_mcbond_it 2.327 r_angle_refined_deg 1.998 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.334 r_dihedral_angle_4_deg 23.568 r_dihedral_angle_3_deg 13.695 r_long_range_B_refined 7.923 r_dihedral_angle_1_deg 5.823 r_scbond_it 4.298 r_mcangle_it 3.273 r_mcbond_it 2.327 r_angle_refined_deg 1.998 r_chiral_restr 0.158 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8894 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 181
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing