2YYG

Crystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YYKPDB ENTRY 2YYK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.5M ammonium sulfate, 0.1M Tris-HCl, 25% (v/v) glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.377α = 90
b = 99.214β = 90
c = 131.537γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2005-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.0000SPring-8BL44B2

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
1247.010.05322.34.3386213862125.304
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)
122.070.1653.63220

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2YYK247.014071138617195083.10.180.202RANDOM32.7
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]
-9.1919.01-9.82
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_angle_deg1.2
c_improper_angle_d0.84
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3734
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms25

Software

Software
Software NamePurpose
HKL-2000data collection
ARP/wARPmodel building
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling