5OST

Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with Gluco-1H-imidazole


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350, ammonium sulphate, Bis-tris
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.617α = 90
b = 54.09β = 90
c = 83.559γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.388.7699.90.3180.1260.9495.57.636706
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3899.71.630.640.74827.5

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 REPLACEMENTTHROUGHOUT5BVU2.188.9744762228698.070.202240.199780.25094RANDOM25.56
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]
-3.292.780.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.658
r_dihedral_angle_4_deg18.103
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg7.12
r_long_range_B_refined4.304
r_long_range_B_other4.303
r_scangle_other2.894
r_mcangle_it2.786
r_mcangle_other2.785
r_scbond_it1.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.658
r_dihedral_angle_4_deg18.103
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg7.12
r_long_range_B_refined4.304
r_long_range_B_other4.303
r_scangle_other2.894
r_mcangle_it2.786
r_mcangle_other2.785
r_scbond_it1.956
r_scbond_other1.956
r_mcbond_it1.91
r_mcbond_other1.91
r_angle_refined_deg1.711
r_angle_other_deg1.038
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms6100
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing