5XXO | pdb_00005xxo

Crystal structure of mutant (D286N) GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with sophorotriose


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
2.3146.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.062α = 90
b = 167.887β = 90
c = 225.45γ = 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
12.025099.60.13115.26.8101477
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.05

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5XXL2.0242.7896343508099.430.17120.169370.180.206250.21RANDOM22.74
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_deg35.962
r_dihedral_angle_4_deg15.797
r_dihedral_angle_3_deg12.87
r_dihedral_angle_1_deg6.463
r_long_range_B_refined3.579
r_long_range_B_other3.539
r_scangle_other2.425
r_mcangle_it1.642
r_mcangle_other1.642
r_scbond_it1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.962
r_dihedral_angle_4_deg15.797
r_dihedral_angle_3_deg12.87
r_dihedral_angle_1_deg6.463
r_long_range_B_refined3.579
r_long_range_B_other3.539
r_scangle_other2.425
r_mcangle_it1.642
r_mcangle_other1.642
r_scbond_it1.46
r_scbond_other1.46
r_angle_refined_deg1.44
r_mcbond_it1.03
r_mcbond_other1.03
r_angle_other_deg0.948
r_chiral_restr0.081
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.005
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 Atoms11447
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing