3WJO

Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli with isopentenyl pyrophosphate (IPP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WJK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.3M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 24% w/v polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4149.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.458α = 90
b = 130.87β = 90
c = 46.412γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

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
12.452599.90.06228.56.327265
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)
12.452.541000.4546.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3WJK2.452526240126796.90.22420.2758RANDOM49.9517
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]
13.799-12.668-1.131
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.978
c_mcangle_it2.408
c_scbond_it2.063
c_mcbond_it1.424
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4638
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms23

Software

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