3ISS

Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A2NPDB entry 1A2N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.150.5 mM sodium phosphite, 1.25 mM UDP-MurNAc, 0.1 M sodium MES, 0.2 M ammonium sulfate, 27% polyethylene glycol 5000 monomethyl ether, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.3848.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.51α = 111.52
b = 120.91β = 104.44
c = 139.73γ = 90.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4rMirror2007-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.1NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.547.4897.60.11774.151673521673521156.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5997.30.4352.94.1816668

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1A2N2.547.4781.96167352167293836797.580.22310.22150.2537Random
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]
4.15531.68793.2756-3.6659-1.2323-0.4894
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.782
f_angle_d1.222
f_chiral_restr0.072
f_bond_d0.011
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms37596
Nucleic Acid Atoms
Solvent Atoms853
Heterogen Atoms576

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling