8DCO

Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from Campylobacter jejuni, serotype HS:42


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7M14PDB entry 7M14

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Protein incubated with 5 mM GDP; precipitant: 7-12% PEG8000, 200 mM potassium chloride, 100 mM MES, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.609α = 90
b = 73.609β = 90
c = 152.346γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2020-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.95098.70.05417.69.633405
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9596.50.3353.45.5

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 REPLACEMENTTHROUGHOUTPDB entry 7M141.936.8331665174098.660.20690.20430.254RANDOM23.329
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.544
r_dihedral_angle_4_deg19.432
r_dihedral_angle_3_deg15.347
r_dihedral_angle_1_deg8.148
r_angle_refined_deg1.656
r_angle_other_deg1.248
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.544
r_dihedral_angle_4_deg19.432
r_dihedral_angle_3_deg15.347
r_dihedral_angle_1_deg8.148
r_angle_refined_deg1.656
r_angle_other_deg1.248
r_chiral_restr0.077
r_bond_refined_d0.008
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 Atoms2951
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing