3KHU

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q3EPDB entry 2Q3E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.1518% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, 10000), 0.1M HEPES pH 7.5, 5% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
3.1560.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.54α = 90
b = 207.34β = 90
c = 93.4γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.348.7499.80.1069.44.31752071751392
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)
12.32.421000.74324.325412

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2Q3E2.348.74175128173128198899.710.195440.195090.2252RANDOM19.743
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]
-3.20.752.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.178
r_dihedral_angle_4_deg20.67
r_dihedral_angle_3_deg13.744
r_scangle_it7.651
r_scbond_it5.293
r_dihedral_angle_1_deg5.28
r_mcangle_it2.975
r_mcbond_it1.593
r_angle_refined_deg1.438
r_angle_other_deg1.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.178
r_dihedral_angle_4_deg20.67
r_dihedral_angle_3_deg13.744
r_scangle_it7.651
r_scbond_it5.293
r_dihedral_angle_1_deg5.28
r_mcangle_it2.975
r_mcbond_it1.593
r_angle_refined_deg1.438
r_angle_other_deg1.007
r_mcbond_other0.326
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21667
Nucleic Acid Atoms
Solvent Atoms1314
Heterogen Atoms515

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling