6B1B

STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI MUTANT XS6 (APO Enzyme)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UM5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291HANGING DROP VAPOR DIFFUSION AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION AND A WELL SOLUTION CONTAINING 1.0 M SUCCINIC ACID, 0.1 M HEPES, AND 1% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 AT PH 7.0. CRYOPROTECTANT WAS MADE BY ADDING 30 % (V/V) GLYCEROL TO THE PRECIPITANT COCKTAIL.
Crystal Properties
Matthews coefficientSolvent content
3.6666.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.455α = 90
b = 100.455β = 90
c = 336.435γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HSROSENBAUM ROCK2017-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-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
11.94446.3699.70.1229.73617.2127481
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)
11.9441.981000.6988.44916.8

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5UM51.94444.531.5127312199999.860.15180.15160.1661
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.537
f_angle_d0.939
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8129
Nucleic Acid Atoms
Solvent Atoms1061
Heterogen Atoms40

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing