1G79

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DNLPDB entry 1DNL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Ammonium sulfate and MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8556.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.72α = 90
b = 63.72β = 90
c = 124.36γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron98IMAGE PLATERIGAKU RAXIS IImirrors2000-03-24LLAUE
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)R Sym 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
125598.10.0560.05112.33.5202022020219.8
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)
122.197.70.2513.33.12659

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1DNL2552019720197103798.90.21140.21140.2080.224RANDOM32.1
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]
3.93.143.9-7.8
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it3.04
c_mcangle_it2.3
c_scbond_it2.15
c_angle_deg1.8
c_mcbond_it1.52
c_improper_angle_d0.83
c_bond_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1642
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms77

Software

Software
Software NamePurpose
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing