3TR2

Structure of a orotidine 5'-phosphate decarboxylase (pyrF) from Coxiella burnetii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelModelArchiveMA-CXT5EENTRY 1LDV that was moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SITTING DROP8.52770.09 M Tris, pH 8.5, 0.17 M sodium acetate, 25.5% PEG4000, 15% glycerol, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.62α = 90
b = 99.676β = 90
c = 110.565γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442011-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
123098.20.05610.94.13114430584-3
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)
122.0394.50.4262.91474

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LDV2.00117.8963267030492153598.030.18450.18450.18280.217RANDOM35.5438
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]
3.6271-1.3553-2.2718
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.146
f_angle_d0.995
f_chiral_restr0.065
f_bond_d0.006
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3354
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms

Software

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