8K2M

Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12 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 sodium Bromide, 0.1 M Bis-Tris 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 = 119.975α = 90
b = 61.608β = 121.43
c = 100.453γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-11-06MSINGLE 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
11.6547.1599.30.9878.86.974805
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)
11.651.680.987

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 REPLACEMENTTHROUGHOUT1.6547.1570898380099.140.16980.168480.1945RANDOM22.76
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]
-0.210.440.22-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.061
r_dihedral_angle_2_deg11.668
r_dihedral_angle_1_deg6.661
r_long_range_B_refined6.113
r_long_range_B_other6.025
r_scangle_other5.147
r_scbond_it3.404
r_scbond_other3.403
r_mcangle_it2.822
r_mcangle_other2.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.061
r_dihedral_angle_2_deg11.668
r_dihedral_angle_1_deg6.661
r_long_range_B_refined6.113
r_long_range_B_other6.025
r_scangle_other5.147
r_scbond_it3.404
r_scbond_other3.403
r_mcangle_it2.822
r_mcangle_other2.822
r_mcbond_it2.006
r_mcbond_other2.005
r_angle_refined_deg1.696
r_angle_other_deg0.593
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms4530
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing