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Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZZ0 PDB ENTRY 1ZZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 600 MM NACL 200 MM NA-CACODYLATE 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.664 α = 90 b = 93.633 β = 103.99 c = 121.664 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 MARRESEARCH 2006-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.9 50 96 0.08 16.9 2.9 111630 2
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 1.9 1.97 93.8 0.36 4.2 2.4
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 1ZZ0 1.9 117.85 106011 5596 96 0.159 0.156 0.1558 0.206 0.206 RANDOM 16.34
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] 0.46 -0.29 -0.62 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.91 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 6.223 r_scangle_it 2.881 r_scbond_it 1.836 r_angle_refined_deg 1.345 r_mcangle_it 1.103 r_mcbond_it 0.626 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.91 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 6.223 r_scangle_it 2.881 r_scbond_it 1.836 r_angle_refined_deg 1.345 r_mcangle_it 1.103 r_mcbond_it 0.626 r_nbtor_refined 0.31 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_refined 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_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 11099 Nucleic Acid Atoms Solvent Atoms 1694 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing