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Crystal structure of HDAC8 in complex with compound 2
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, 0.06M Gly-Gly-Gly, 4mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.75 α = 90 b = 91.29 β = 94.09 c = 92.7 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 MARMOSAIC 300 mm CCD 2014-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.993 APS 21-ID-D
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 2.88 50 99.8 0.112 10.9 3.79 29616
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 2.88 2.95 99.8 3.83
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 2.88 50 29616 1521 93.73 0.20129 0.1988 0.24875 0.231 RANDOM 56.341
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] 0.22 1.53 0.57 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.967 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_4_deg 11.948 r_dihedral_angle_1_deg 6.095 r_long_range_B_other 4.706 r_long_range_B_refined 4.705 r_scangle_other 1.574 r_mcangle_it 1.54 r_mcangle_other 1.54 r_angle_refined_deg 1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.967 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_4_deg 11.948 r_dihedral_angle_1_deg 6.095 r_long_range_B_other 4.706 r_long_range_B_refined 4.705 r_scangle_other 1.574 r_mcangle_it 1.54 r_mcangle_other 1.54 r_angle_refined_deg 1.237 r_scbond_it 1.056 r_scbond_other 1.052 r_angle_other_deg 0.911 r_mcbond_it 0.853 r_mcbond_other 0.852 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8411 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing