3MCM

Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase dihydropteroate synthase bifunctional enzyme from Francisella tularensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QX0PDB entries 2QX0, 1TWW
experimental modelPDB 1TWWPDB entries 2QX0, 1TWW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8291TRIS, Na Acetate, PEG 4000, Glyerol, pH 8.0, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.821α = 91.13
b = 57.779β = 99.39
c = 105.127γ = 111.64
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.238.694.40.1323.63.546769441402
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)
2.22.27880.10.285.32.93743

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 2QX0, 1TWW2.238.4421.9644083222594.180.2190.2150.278random41.898
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]
-0.4780.0810.273-0.317-0.4220.795
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.317
f_angle_d1.127
f_chiral_restr0.076
f_bond_d0.008
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6021
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling