1JNW

Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298potassium phosphate, ammonium phosphate, mercaptoethanol, N-morpholinoethanesulfonate, dioxane, pyridoxal 5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.358α = 90
b = 52.238β = 101.45
c = 53.913γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IImirrors2000-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.074496.60.0778.32.413991135101125.2
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)
12.072.1492.90.2642.1

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 1dnl with omission of all waters, ligands and ions2.0744.01135101351068496.40.1820.1780.1780.231RANDOM28.4
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]
-2.2-0.278.07-5.87
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it2.45
c_scbond_it1.67
c_mcangle_it1.65
c_angle_deg1.5
c_mcbond_it1.01
c_improper_angle_d0.94
c_bond_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1775
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms52

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
bioteXdata reduction
bioteXdata scaling