2POQ

Dimeric Dihydrodiol Dehydrogenase complexed with inhibitor, Isoascorbic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52952M ammonium sulphate, 0.1 sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.6266.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.832α = 90
b = 122.832β = 90
c = 121.293γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2003-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.592099.2616.5172561712812
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.592.68983.6284

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2O4U2.59204171281626486498.830.20240.170350.166990.2341RANDOM27.089
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]
0.420.210.42-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.885
r_dihedral_angle_4_deg19.506
r_dihedral_angle_3_deg18.7
r_dihedral_angle_1_deg6.509
r_scangle_it4.843
r_scbond_it3.065
r_angle_refined_deg2.105
r_mcangle_it1.783
r_mcbond_it1.062
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.885
r_dihedral_angle_4_deg19.506
r_dihedral_angle_3_deg18.7
r_dihedral_angle_1_deg6.509
r_scangle_it4.843
r_scbond_it3.065
r_angle_refined_deg2.105
r_mcangle_it1.783
r_mcbond_it1.062
r_nbtor_refined0.317
r_nbd_refined0.233
r_xyhbond_nbd_refined0.192
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.147
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2529
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms36

Software

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