2XVL

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with Pentaerythritol propoxylate (5 4 PO OH)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G3MPDB ENTRY 2G3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1740 % PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.1 M BIS-TRIS (PH 7.0), 5 MM NI SO4
Crystal Properties
Matthews coefficientSolvent content
3.5365.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.653α = 90
b = 157.653β = 90
c = 226.688γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2009-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.358.51000.1716.311.374143-324.33
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)
12.32.421000.477.54.5

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 2G3M2.354.5481.3874143373699.990.1470.1450.1853
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]
2.84392.8439-5.6878
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.183
f_angle_d1.043
f_chiral_restr0.07
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7572
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms50

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing