6ZL6

Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U4Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8293200 mM potassium acetate and 14-24% PEG 3350, 2 mM NAD+
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.482α = 96.77
b = 58.56β = 98.41
c = 64.904γ = 110.3
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.98SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.745.35930.9910.21.755496
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.740.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5U4Q1.745.3555496287292.960.17220.17070.2025RANDOM25.573
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]
-0.270.42-0.340.20.82-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.125
r_dihedral_angle_3_deg13.828
r_dihedral_angle_4_deg12.585
r_dihedral_angle_1_deg6.908
r_angle_refined_deg1.675
r_angle_other_deg1.415
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.125
r_dihedral_angle_3_deg13.828
r_dihedral_angle_4_deg12.585
r_dihedral_angle_1_deg6.908
r_angle_refined_deg1.675
r_angle_other_deg1.415
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4932
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing