8E0X

DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 5 mM DAHP oxime, 5 mM phosphoenolpyruvate, 5 mM erythrose 4-pohsphate, 30% (v/v) ethylene glycol, 1:1:0.2
Crystal Properties
Matthews coefficientSolvent content
2.4950.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.717α = 90
b = 53.181β = 115.795
c = 150.366γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9767.6599.80.050.0580.030.99917.73.610537629.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0599.90.420.4920.2540.8843.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5CKS1.9743.481.34105290199999.120.18820.18770.214140.64
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.3003
f_angle_d1.0551
f_chiral_restr0.0623
f_bond_d0.008
f_plane_restr0.0078
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10231
Nucleic Acid Atoms
Solvent Atoms1007
Heterogen Atoms53

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing