6JXL

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
1EVAPORATION628020%PEG 8000, 0.2M NaI,0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.3547.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.54α = 90
b = 58.969β = 90
c = 69.502γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray280CCDADSC 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
11.344.96580.0414.75.53905713.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3471.7

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 REPLACEMENTTHROUGHOUT2DFC1.332.671.3439039199780.040.1530.15210.167718.7787
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_d12.288
f_angle_d1.567
f_chiral_restr0.108
f_bond_d0.014
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1472
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms57

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing