2YVW

Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UAEPDB ENTRY 1UAE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.429140% (v/v) PEG 400, 0.1M Imidazole, pH 7.4, MICRO BATCH, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.0960.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.004α = 90
b = 132.004β = 90
c = 58.165γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102007-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
11.815098.70.06733.4710.45228314.2
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)
11.811.8790.80.3296.248.9

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 1UAE1.8143.64502732516950.1950.1950.22RANDOM23.6
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]
-9.42-3.03-9.4218.84
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it3.17
c_scbond_it2.11
c_mcangle_it1.5
c_angle_deg1.2
c_mcbond_it1.04
c_improper_angle_d0.71
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.6
c_scangle_it3.17
c_scbond_it2.11
c_mcangle_it1.5
c_angle_deg1.2
c_mcbond_it1.04
c_improper_angle_d0.71
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3252
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms49

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing