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Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with SAHA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NVR PDB entry 2NVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 20 % PEG 3350, 0.1 M HEPES pH 7.5, 10 % Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.825 α = 90 b = 81.825 β = 90 c = 148.867 γ = 120
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 315 2006-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10000 NSLS X25
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 2.1 50 93.5 0.049 23.8 3.2 60749 60749
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) 2.1 2.18 86.4 0.277 3.7 2.3 6428
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 2NVR 2.1 40 57634 3080 93.41 0.19903 0.19664 0.1944 0.24291 0.2416 RANDOM 37.023
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] 1.67 0.83 1.67 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_3_deg 18.055 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.972 r_scbond_it 2.637 r_mcangle_it 1.715 r_angle_refined_deg 1.707 r_mcbond_it 0.996 r_metal_ion_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_3_deg 18.055 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.972 r_scbond_it 2.637 r_mcangle_it 1.715 r_angle_refined_deg 1.707 r_mcbond_it 0.996 r_metal_ion_refined 0.338 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8400 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing ARP/wARP model building