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Crystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary complex with NADP and 18beta-glycyrrhetinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VNA PDB ENTRY 2VNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M TRIS PH 8.5; 2M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.374 α = 90 b = 84.11 β = 109.05 c = 72.888 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU IMAGE PLATE OSMIC 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 68.9 99 0.1 4 25301 2
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 2VNA 2 68.84 25301 1341 99.4 0.18 0.177 0.1865 0.223 0.2273 RANDOM 15.72
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] -0.06 -0.11 0.29 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.285 r_dihedral_angle_4_deg 12.684 r_dihedral_angle_3_deg 12.145 r_scangle_it 6.737 r_dihedral_angle_1_deg 5.767 r_scbond_it 5.118 r_mcangle_it 2.913 r_mcbond_it 1.878 r_angle_refined_deg 1.413 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.285 r_dihedral_angle_4_deg 12.684 r_dihedral_angle_3_deg 12.145 r_scangle_it 6.737 r_dihedral_angle_1_deg 5.767 r_scbond_it 5.118 r_mcangle_it 2.913 r_mcbond_it 1.878 r_angle_refined_deg 1.413 r_angle_other_deg 0.835 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2652 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing