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Crystal structure of HDAC8-inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W22 PDB ENTRY 1W22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP HDAC8 POINT MUTANT Y306F, IN 50 MM TRIS-HCL PH 8.0, 5% GLYCEROL, 1 MM DTT, 150 MM KCL, WAS CONCENTRATED TO 217 UM, RESPECTIVELY. Y306F-HDAC8 PLUS 15 MOLAR EXCESSES OF SUBSTRATE, WAS CRYSTALLIZED AT RT BY THE HANGING-DROP METHOD IN 50 MM TRIS-HCL PH 8.0, 50 MM MGCL2, 10% PEG 4,000, 2 MM TRI(2-CARBOXYETHYL)PHOSPHIN (TCEP) AND 30 MM GLYCYL-GLYCYL-GLYCINE.
Crystal Properties Matthews coefficient Solvent content 2.72 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.298 α = 90 b = 98.694 β = 90 c = 110.474 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.25 74.53 98.7 0.09 16.8 6.3 44426 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 98.1 0.6 3.1 6.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W22 2.25 50 41545 2203 98.5 0.198 0.196 0.2029 0.24 RANDOM 35.83
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] 0.31 -3.53 3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.467 r_scangle_it 2.979 r_scbond_it 1.75 r_angle_refined_deg 1.42 r_mcangle_it 1.261 r_angle_other_deg 1.001 r_mcbond_it 0.658 r_symmetry_vdw_refined 0.331 r_symmetry_hbond_refined 0.256 r_nbd_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.467 r_scangle_it 2.979 r_scbond_it 1.75 r_angle_refined_deg 1.42 r_mcangle_it 1.261 r_angle_other_deg 1.001 r_mcbond_it 0.658 r_symmetry_vdw_refined 0.331 r_symmetry_hbond_refined 0.256 r_nbd_other 0.235 r_nbd_refined 0.227 r_symmetry_vdw_other 0.225 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.088 r_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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_other r_long_range_B_refined 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 5613 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing