2ZXQ

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92930.1M MES-NaOH, 3% PEG 20000, 25% MPD, 0.2M NaCl, 0.01M MnCl2, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.3871.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.267α = 90
b = 192.267β = 90
c = 123.017γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-02-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.96787, 0.97923, 0.97939, 0.96416Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
125099.10.07527.27.217408917244727.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0799.80.4673.56.517314

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT236.49172447163203859898.710.173240.172030.19564RANDOM30.743
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]
0.030.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg16.375
r_dihedral_angle_3_deg13.409
r_dihedral_angle_1_deg6.655
r_scangle_it3.285
r_scbond_it2.14
r_angle_refined_deg1.408
r_mcangle_it1.362
r_mcbond_it0.842
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg16.375
r_dihedral_angle_3_deg13.409
r_dihedral_angle_1_deg6.655
r_scangle_it3.285
r_scbond_it2.14
r_angle_refined_deg1.408
r_mcangle_it1.362
r_mcbond_it0.842
r_nbtor_refined0.304
r_nbd_refined0.196
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.132
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9070
Nucleic Acid Atoms
Solvent Atoms1427
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing