6Q7J

GH3 exo-beta-xylosidase (XlnD) in complex with xylobiose aziridine activity based probe


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Halogens NaF; NaBr; NaI; imidazole/MES pH 6.5, PEG550/PEG20K.
Crystal Properties
Matthews coefficientSolvent content
2.3647.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.398α = 90
b = 91.579β = 90
c = 245.059γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1446.261000.2620.0974.48.288380
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.180.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1446.2683847444399.930.199230.195660.26799RANDOM46.099
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]
-1.875.99-4.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.776
r_dihedral_angle_4_deg16.661
r_dihedral_angle_3_deg15.013
r_dihedral_angle_1_deg7.252
r_long_range_B_refined6.916
r_long_range_B_other6.916
r_scangle_other5.235
r_mcangle_it5.098
r_mcangle_other5.098
r_mcbond_it3.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.776
r_dihedral_angle_4_deg16.661
r_dihedral_angle_3_deg15.013
r_dihedral_angle_1_deg7.252
r_long_range_B_refined6.916
r_long_range_B_other6.916
r_scangle_other5.235
r_mcangle_it5.098
r_mcangle_other5.098
r_mcbond_it3.575
r_mcbond_other3.574
r_scbond_it3.494
r_scbond_other3.494
r_angle_refined_deg1.633
r_angle_other_deg1.268
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11701
Nucleic Acid Atoms
Solvent Atoms541
Heterogen Atoms546

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing