2XVK

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1725 % PEG MONOMETHYL ETHER 550 (PEG MME 550), 0.1 M BIS-TRIS (PH 7.0)
Crystal Properties
Matthews coefficientSolvent content
3.564.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.524α = 90
b = 156.524β = 90
c = 227.762γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2009-11-28MSINGLE 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
12.550990.0710.110.157181-3
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)
12.52.5499.90.7528

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 2G3M2.50349.9851.3457181290499.760.19720.19490.2397
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]
7.75677.7567-15.5134
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.366
f_angle_d1.1
f_chiral_restr0.075
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7572
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms15

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing