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Crystal structure of catalytic domain of human histone deacetylase HDAC7
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 13 % PEG 3350, 0.1 M HEPES pH 7.5, 10 % Isopropanol, 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.75 α = 90 b = 81.75 β = 90 c = 148.895 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 2006-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 98.1 0.056 33 5.4 65508 64241 -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) 2.1 2.18 85.3 0.419 2.6 3.9 5579
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 34.44 60432 3222 98.09 0.20499 0.20174 0.1979 0.26404 0.2558 RANDOM 43.494
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_4_deg 18.497 r_dihedral_angle_3_deg 18.131 r_dihedral_angle_1_deg 6.948 r_scangle_it 4.055 r_scbond_it 2.685 r_mcangle_it 1.793 r_angle_refined_deg 1.787 r_mcbond_it 1.011 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_4_deg 18.497 r_dihedral_angle_3_deg 18.131 r_dihedral_angle_1_deg 6.948 r_scangle_it 4.055 r_scbond_it 2.685 r_mcangle_it 1.793 r_angle_refined_deg 1.787 r_mcbond_it 1.011 r_nbtor_refined 0.308 r_metal_ion_refined 0.286 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.17 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8429 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing