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Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MAX PDB entry 3MAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.034 α = 90 b = 97.49 β = 90 c = 138.922 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 MARMOSAIC 225 mm CCD 2011-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 1.57 50 100 0.074 21 5.6 174095 18.9
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 1.57 1.63 100 0.587 3.1 5.5
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 3MAX 1.57 33.57 174095 8703 99.94 0.17 0.1691 0.1694 0.1874 0.189 RANDOM 22.7
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] 3.3686 -6.5864 3.2178
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.66 t_omega_torsion 3.7 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.66 t_omega_torsion 3.7 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8869 Nucleic Acid Atoms Solvent Atoms 846 Heterogen Atoms 201
Software Software Software Name Purpose PHASER phasing BUSTER refinement HKL-2000 data reduction SCALEPACK data scaling