8K2H

Crystal structure of Group 2Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GalNAc-thiazoline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.2 M Magnesium chloride hexahydrate, 0.1 M Hepes-Na pH 7.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.3848.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.852α = 90
b = 134.036β = 90
c = 149.969γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0000SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.248.071000.9979.513.671289
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.250.648

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 REPLACEMENTTHROUGHOUT2.248.0767508369099.950.172060.168920.22947RANDOM43.8
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]
2.97-2.87-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.927
r_dihedral_angle_2_deg16.81
r_long_range_B_other10.286
r_long_range_B_refined10.275
r_scangle_other8.613
r_dihedral_angle_1_deg7.964
r_mcangle_other7.18
r_mcangle_it7.179
r_scbond_it6.551
r_scbond_other6.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.927
r_dihedral_angle_2_deg16.81
r_long_range_B_other10.286
r_long_range_B_refined10.275
r_scangle_other8.613
r_dihedral_angle_1_deg7.964
r_mcangle_other7.18
r_mcangle_it7.179
r_scbond_it6.551
r_scbond_other6.55
r_mcbond_it5.558
r_mcbond_other5.558
r_angle_refined_deg2.11
r_angle_other_deg0.686
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms8941
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing