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Crystal structure of HDAC8 in complex with compound 30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 291 0.1M MES pH5.3, 5% PEG6000, 0.14 M Gly-Gly-Gly, 2mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.54 α = 90 b = 91.161 β = 94.07 c = 92.574 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2017-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.99 SSRF BL18U1
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 2.8 50 99.8 0.0125 14.8 3.4 35823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.9 1.5 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1t64 2.8 50 34035 1768 99.11 0.19642 0.1944 0.23577 0.2267 RANDOM 76.315
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] 4.14 -3.68 -0.92 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.546 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_4_deg 13.926 r_long_range_B_other 10.956 r_long_range_B_refined 10.951 r_scangle_other 8.018 r_mcangle_other 7.797 r_mcangle_it 7.792 r_dihedral_angle_1_deg 6.354 r_mcbond_it 5.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.546 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_4_deg 13.926 r_long_range_B_other 10.956 r_long_range_B_refined 10.951 r_scangle_other 8.018 r_mcangle_other 7.797 r_mcangle_it 7.792 r_dihedral_angle_1_deg 6.354 r_mcbond_it 5.164 r_scbond_it 5.158 r_scbond_other 5.157 r_mcbond_other 5.143 r_angle_refined_deg 1.452 r_angle_other_deg 0.966 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8476 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing