8WN5

Crystal structure of GH1 beta-glucosidase Td2F2 E352Q glucose complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP303CHES, K/Na tartrate, LiSO4
Crystal Properties
Matthews coefficientSolvent content
2.2846.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.608α = 90
b = 69.24β = 90
c = 96.683γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2023-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.548.421000.0250.0350.0250.99824.31.973302
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531000.0680.0960.0680.9779.61.9

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 REPLACEMENTTHROUGHOUT1.548.4269515378699.990.171380.17060.18541RANDOM8.278
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]
0.790.01-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.647
r_dihedral_angle_2_deg6.688
r_dihedral_angle_1_deg6.481
r_long_range_B_refined4.111
r_long_range_B_other4.111
r_scangle_other3.048
r_scbond_it2.026
r_scbond_other2.026
r_angle_refined_deg1.843
r_mcangle_it1.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.647
r_dihedral_angle_2_deg6.688
r_dihedral_angle_1_deg6.481
r_long_range_B_refined4.111
r_long_range_B_other4.111
r_scangle_other3.048
r_scbond_it2.026
r_scbond_other2.026
r_angle_refined_deg1.843
r_mcangle_it1.832
r_mcangle_other1.832
r_mcbond_it1.166
r_mcbond_other1.165
r_angle_other_deg0.631
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms3475
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing