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Crystal structure of HDAC8-substrate 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 2.21 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.304 α = 90 b = 151.801 β = 117.02 c = 57.552 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 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 50 95.6 0.05 18.2 4.8 53718 3
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 2.06 59.4 0.15 6.1 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W22 2 50 49636 2651 97.5 0.179 0.176 0.1841 0.23 0.2331 RANDOM 18.7
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] -0.06 0.3 0.25 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.361 r_scangle_it 3.39 r_scbond_it 2.071 r_angle_refined_deg 1.433 r_mcangle_it 1.188 r_angle_other_deg 0.914 r_mcbond_it 0.647 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.259 r_nbd_other 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.361 r_scangle_it 3.39 r_scbond_it 2.071 r_angle_refined_deg 1.433 r_mcangle_it 1.188 r_angle_other_deg 0.914 r_mcbond_it 0.647 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.259 r_nbd_other 0.241 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.176 r_nbtor_other 0.103 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 5819 Nucleic Acid Atoms Solvent Atoms 746 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing