8K2N

Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaLy from Lacticaseibacillus yichunensis, apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M sodium acetate pH 4.2, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.2962.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.93α = 70.93
b = 94.62β = 73.81
c = 116.18γ = 72.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-10-23MSINGLE 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
12.549.011000.9637.12107859
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)
12.52.540.672

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 REPLACEMENTTHROUGHOUT2.548.79102572528799.990.185560.182660.24147RANDOM23.624
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]
-0.50.350.781.770.24-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.04
r_dihedral_angle_2_deg15.378
r_dihedral_angle_1_deg7.854
r_long_range_B_refined6.382
r_long_range_B_other6.37
r_scangle_other4.8
r_mcangle_it4.37
r_mcangle_other4.37
r_scbond_it3.344
r_scbond_other3.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.04
r_dihedral_angle_2_deg15.378
r_dihedral_angle_1_deg7.854
r_long_range_B_refined6.382
r_long_range_B_other6.37
r_scangle_other4.8
r_mcangle_it4.37
r_mcangle_other4.37
r_scbond_it3.344
r_scbond_other3.344
r_mcbond_it2.98
r_mcbond_other2.98
r_angle_refined_deg2.107
r_angle_other_deg0.689
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.011
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 Atoms17040
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing