6ZLL

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5277200 mM potassium acetate, 14-24% PEG3350, 2 mM NAD+, 2 mM UDP-Galacturonic acid
Crystal Properties
Matthews coefficientSolvent content
2.5351.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.787α = 91.92
b = 62.652β = 99.86
c = 105.712γ = 91.98
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
11.8546.09930.998.76.9107680
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)
11.851.8980.46

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 REPLACEMENTTHROUGHOUT5U4Q1.8546.09107680559592.540.18880.1870.2217RANDOM37.109
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]
1.321.971.32-0.420.71-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg15.85
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg7.107
r_angle_refined_deg1.58
r_angle_other_deg1.325
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg15.85
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg7.107
r_angle_refined_deg1.58
r_angle_other_deg1.325
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9984
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms324

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing