6JUG

Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DFC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6291PEG 8000, 0.2M NaI,0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.4148.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.379α = 90
b = 59.14β = 90
c = 69.851γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 315r2018-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11.0SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.1937.4597.9419.66635939.93
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.23391.91

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 REPLACEMENTTHROUGHOUT2DFC1.1937.4461.3463593320497.940.13430.13380.144113.8832
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_d12.451
f_angle_d1.375
f_chiral_restr0.111
f_bond_d0.011
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1473
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms3

Software

Software
Software NamePurpose
XDSdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing