2O3J

Structure of Caenorhabditis Elegans UDP-Glucose Dehydrogenase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290200 MM MgCl2, 100 MM BIS-TRIS, PH 5.50, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.856.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.716α = 90
b = 144.092β = 123.24
c = 92.072γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2006-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.885098.70.0640.0572.72.713325434.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9590.40.730.710.82.125057

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 1DLI1.8820133254133254414598.170.21020.208580.26315RANDOM45.475
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]
-2.26-1.111.47-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.866
r_dihedral_angle_3_deg17.826
r_dihedral_angle_4_deg14.668
r_scangle_it9.903
r_dihedral_angle_1_deg7.534
r_scbond_it7.42
r_mcangle_it6.026
r_mcbond_it4.874
r_angle_refined_deg1.114
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.866
r_dihedral_angle_3_deg17.826
r_dihedral_angle_4_deg14.668
r_scangle_it9.903
r_dihedral_angle_1_deg7.534
r_scbond_it7.42
r_mcangle_it6.026
r_mcbond_it4.874
r_angle_refined_deg1.114
r_nbtor_refined0.307
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.175
r_nbd_refined0.174
r_symmetry_vdw_refined0.156
r_chiral_restr0.104
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms10719
Nucleic Acid Atoms
Solvent Atoms844
Heterogen Atoms54

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling