8WNA

Crystal structure of GH1 beta-glucosidase Td2F2 E352Q laminaribiose complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WH5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5303CHES, K/Na tartrate, LiSO4
Crystal Properties
Matthews coefficientSolvent content
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.41α = 90
b = 68.416β = 90
c = 95.988γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2023-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
11.1648.4299.90.0380.0410.0160.99925.76.4155824
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)
11.161.1898.80.2540.2830.1230.95865

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 REPLACEMENTTHROUGHOUT1.1648.42148291743799.890.15140.150740.16398RANDOM10.876
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_3_deg13.602
r_dihedral_angle_2_deg7.017
r_dihedral_angle_1_deg6.511
r_long_range_B_refined4.311
r_long_range_B_other4.31
r_scangle_other3.474
r_scbond_it2.409
r_scbond_other2.409
r_mcangle_other2.005
r_mcangle_it2.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.602
r_dihedral_angle_2_deg7.017
r_dihedral_angle_1_deg6.511
r_long_range_B_refined4.311
r_long_range_B_other4.31
r_scangle_other3.474
r_scbond_it2.409
r_scbond_other2.409
r_mcangle_other2.005
r_mcangle_it2.004
r_angle_refined_deg1.907
r_mcbond_it1.318
r_mcbond_other1.316
r_angle_other_deg0.638
r_chiral_restr0.108
r_bond_refined_d0.016
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 Atoms344
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing