5XXM

Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298PEG 3350 Sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.346.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.82α = 90
b = 167.69β = 90
c = 224.9γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
11.742.793.60.10610.36158119
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.73

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 REPLACEMENTTHROUGHOUT1.742.7150173786593.430.182590.181270.20775RANDOM16.294
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg15.344
r_dihedral_angle_3_deg12.866
r_dihedral_angle_1_deg6.324
r_long_range_B_refined3.191
r_long_range_B_other2.887
r_scangle_other1.486
r_angle_refined_deg1.296
r_mcangle_it1.124
r_mcangle_other1.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg15.344
r_dihedral_angle_3_deg12.866
r_dihedral_angle_1_deg6.324
r_long_range_B_refined3.191
r_long_range_B_other2.887
r_scangle_other1.486
r_angle_refined_deg1.296
r_mcangle_it1.124
r_mcangle_other1.124
r_angle_other_deg0.917
r_scbond_it0.884
r_scbond_other0.884
r_mcbond_it0.658
r_mcbond_other0.658
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms11559
Nucleic Acid Atoms
Solvent Atoms1133
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
MOLREPphasing