5WZR

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.02M MgCl2, 0.1M HEPES-NaOH, 7.5% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.628α = 90
b = 128.478β = 90
c = 176.885γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2016-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.1000Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.79103.9599.70.05719.66.337110
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.851000.5180.9792.46.7

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 DIFFRACTIONSADTHROUGHOUT2.79103.9535202185298.660.233150.228990.31325RANDOM79.962
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]
0.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.383
r_dihedral_angle_4_deg18.17
r_dihedral_angle_3_deg16.76
r_long_range_B_other10.608
r_long_range_B_refined10.607
r_dihedral_angle_1_deg8.013
r_mcangle_it7.72
r_mcangle_other7.72
r_scangle_other6.606
r_mcbond_it4.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.383
r_dihedral_angle_4_deg18.17
r_dihedral_angle_3_deg16.76
r_long_range_B_other10.608
r_long_range_B_refined10.607
r_dihedral_angle_1_deg8.013
r_mcangle_it7.72
r_mcangle_other7.72
r_scangle_other6.606
r_mcbond_it4.863
r_mcbond_other4.855
r_scbond_it4.027
r_scbond_other4.027
r_angle_refined_deg1.461
r_angle_other_deg0.858
r_chiral_restr0.078
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
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 Atoms9972
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing