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Crystal Structure of Mammalian Dimeric Dihydrodiol Dehydrogenase in complex with Dihydroxyacetone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4U PDB ENTRY 2O4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 2M ammonium sulfate, 0.1M Tris, pH 8.5, 8% PEG 8000, Vapor Diffusion, Hanging Drop, Temperature 295K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.6 65.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.446 α = 90 b = 122.446 β = 90 c = 121.388 γ = 120
Symmetry Space Group P 61 2 2
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 MAR scanner 345 mm plate Mirrors 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54179
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 30 98.74 0.0571 14.2 6.65 39010 38518 1 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 85.1 0.3863 1.6 5.43 3343
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 2O4U 1.9 29.41 1 39010 38518 1991 98.74 0.16325 0.1611 0.1843 0.2051 0.1824 RANDOM 26.654
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] 0.26 0.13 0.26 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 18.764 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 5.829 r_scangle_it 4.886 r_scbond_it 3.281 r_angle_refined_deg 1.976 r_mcangle_it 1.924 r_mcbond_it 1.214 r_chiral_restr 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.679 r_dihedral_angle_4_deg 18.764 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 5.829 r_scangle_it 4.886 r_scbond_it 3.281 r_angle_refined_deg 1.976 r_mcangle_it 1.924 r_mcbond_it 1.214 r_chiral_restr 0.164 r_bond_refined_d 0.026 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling