6ZLK

Equilibrium Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Glucuronic acid/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 DIFFUSION7277200 mM potassium acetate, 14-24% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.737α = 90
b = 124.349β = 90.63
c = 98.364γ = 90
Symmetry
Space GroupP 1 21 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
11.549.37970.9973.8190286
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)
11.51.530.3

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 REPLACEMENTTHROUGHOUT5U4Q1.549.371902861001897.340.17360.17210.2035RANDOM23.947
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]
-0.650.50.68-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.073
r_dihedral_angle_4_deg14.016
r_dihedral_angle_3_deg12.983
r_dihedral_angle_1_deg6.823
r_angle_refined_deg1.722
r_angle_other_deg1.481
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.073
r_dihedral_angle_4_deg14.016
r_dihedral_angle_3_deg12.983
r_dihedral_angle_1_deg6.823
r_angle_refined_deg1.722
r_angle_other_deg1.481
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9867
Nucleic Acid Atoms
Solvent Atoms934
Heterogen Atoms472

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing