3O6D

Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82890.056 M sodium phosphate, 1.344 di-potassium phosphate, (10 mM PYRIDOXINE-5'-PHOSPHATE was used for crystal soaking), pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.754.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.239α = 90
b = 90.239β = 90
c = 156.081γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-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
11.9531.999.90.0711.26.8239442394442.5
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)
1.951.981000.7742.376.81178

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.95322384123841122499.550.17140.17140.170.1971RANDOM38.428
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]
1.341.34-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.303
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg15.146
r_dihedral_angle_1_deg5.656
r_scangle_it4.617
r_scbond_it2.873
r_mcangle_it1.67
r_angle_refined_deg1.594
r_angle_other_deg0.95
r_mcbond_it0.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.303
r_dihedral_angle_4_deg15.215
r_dihedral_angle_3_deg15.146
r_dihedral_angle_1_deg5.656
r_scangle_it4.617
r_scbond_it2.873
r_mcangle_it1.67
r_angle_refined_deg1.594
r_angle_other_deg0.95
r_mcbond_it0.915
r_mcbond_other0.266
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2052
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing