2QZ2

Crystal structure of a glycoside hydrolase family 11 xylanase from Aspergillus niger in complex with xylopentaose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52771.6M ammonium sulphate, 0.1M HEPES pH 7.5, 0.1 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.7354.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.326α = 90
b = 67.326β = 90
c = 165.401γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.9918EMBL/DESY, HamburgBW7A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.83098.20.09413.76010584321.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.8598.20.3025.3271

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UKR2.819.485220521954297.310.226320.22120.27678RANDOM23.812
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]
0.040.710.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.048
r_dihedral_angle_4_deg31.141
r_dihedral_angle_3_deg13.951
r_dihedral_angle_1_deg6.212
r_angle_refined_deg1.005
r_sphericity_free0.931
r_scangle_it0.595
r_mcangle_it0.564
r_scbond_it0.356
r_rigid_bond_restr0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.048
r_dihedral_angle_4_deg31.141
r_dihedral_angle_3_deg13.951
r_dihedral_angle_1_deg6.212
r_angle_refined_deg1.005
r_sphericity_free0.931
r_scangle_it0.595
r_mcangle_it0.564
r_scbond_it0.356
r_rigid_bond_restr0.333
r_mcbond_it0.312
r_nbtor_refined0.31
r_sphericity_bonded0.267
r_nbd_refined0.177
r_symmetry_hbond_refined0.168
r_symmetry_vdw_refined0.139
r_xyhbond_nbd_refined0.118
r_chiral_restr0.064
r_metal_ion_refined0.008
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_mcbond_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_bond_other_d
r_metal_ion_other
r_nbtor_other
r_nbd_other
r_gen_planes_other
r_symmetry_vdw_other
r_angle_other_deg
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1402
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing