5Z5I

Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with L-arabinose and D-xylose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72830.1M HEPES (N-(2-hydroxyethyl)piperazine-N-(2-ethanesulfonic acid)) buffer, pH 7.0, 5% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.816α = 90
b = 59.816β = 90
c = 277.87γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.69541.937990.0720.0770.02817.77.557020
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7993.10.2730.2730.3030.1282.65.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1yif1.741.8554015286098.920.16080.15920.1905RANDOM16.832
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]
0.420.42-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.031
r_dihedral_angle_4_deg14.848
r_dihedral_angle_3_deg13.199
r_dihedral_angle_1_deg6.789
r_angle_refined_deg1.44
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4053
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms41

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
COMBATdata reduction
PHASERphasing