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Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with Trichostatin A (TSA)
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 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.827 α = 90 b = 81.827 β = 90 c = 148.97 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 50 97.5 0.041 26.3 3.1 73439 73439
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 2.07 79 0.238 3.6 2.5 6619
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 35.42 69791 3651 97.47 0.20428 0.20126 0.1988 0.26312 0.2612 RANDOM 36.648
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.708 r_dihedral_angle_4_deg 19.447 r_dihedral_angle_3_deg 17.874 r_dihedral_angle_1_deg 7.388 r_scangle_it 4.007 r_scbond_it 2.656 r_angle_refined_deg 1.689 r_mcangle_it 1.678 r_mcbond_it 1.001 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.708 r_dihedral_angle_4_deg 19.447 r_dihedral_angle_3_deg 17.874 r_dihedral_angle_1_deg 7.388 r_scangle_it 4.007 r_scbond_it 2.656 r_angle_refined_deg 1.689 r_mcangle_it 1.678 r_mcbond_it 1.001 r_nbtor_refined 0.306 r_metal_ion_refined 0.283 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.124 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 8424 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 78
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