3OHS

Crystal Structure of Mammalian Dimeric Dihydrodiol Dehydrogenase in complex with Dihydroxyacetone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O4UPDB ENTRY 2O4U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52952M ammonium sulfate, 0.1M Tris, pH 8.5, 8% PEG 8000, Vapor Diffusion, Hanging Drop, Temperature 295K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
3.665.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.446α = 90
b = 122.446β = 90
c = 121.388γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrors2008-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.93098.740.057114.26.65390103851812
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9785.10.38631.65.433343

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2O4U1.929.4113901038518199198.740.163250.16110.2051RANDOM26.654
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]
0.260.130.26-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.679
r_dihedral_angle_4_deg18.764
r_dihedral_angle_3_deg16.026
r_dihedral_angle_1_deg5.829
r_scangle_it4.886
r_scbond_it3.281
r_angle_refined_deg1.976
r_mcangle_it1.924
r_mcbond_it1.214
r_chiral_restr0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.679
r_dihedral_angle_4_deg18.764
r_dihedral_angle_3_deg16.026
r_dihedral_angle_1_deg5.829
r_scangle_it4.886
r_scbond_it3.281
r_angle_refined_deg1.976
r_mcangle_it1.924
r_mcbond_it1.214
r_chiral_restr0.164
r_bond_refined_d0.026
r_gen_planes_refined0.01
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 AtomsNumber
Protein Atoms2529
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms50

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling