5XXN

Crystal Structure of mutant (D286N) beta-glucosidase from Bacteroides thetaiotaomicron in complex with sophorose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XXL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298PEG 3350 Sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.346.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.977α = 90
b = 167.909β = 90
c = 225.061γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
12.055096.40.15911.75.794130
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5XXL2.0546.7489282479696.190.18050.178410.21944RANDOM22.481
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.924
r_dihedral_angle_4_deg16.679
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg6.636
r_long_range_B_refined3.486
r_long_range_B_other3.44
r_scangle_other2.356
r_mcangle_it1.617
r_mcangle_other1.617
r_angle_refined_deg1.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.924
r_dihedral_angle_4_deg16.679
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg6.636
r_long_range_B_refined3.486
r_long_range_B_other3.44
r_scangle_other2.356
r_mcangle_it1.617
r_mcangle_other1.617
r_angle_refined_deg1.458
r_scbond_it1.434
r_scbond_other1.434
r_mcbond_it1.022
r_mcbond_other1.022
r_angle_other_deg0.96
r_chiral_restr0.084
r_bond_refined_d0.01
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 Atoms11450
Nucleic Acid Atoms
Solvent Atoms765
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing