5BX4

Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with Glucoimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BVU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52880.16 M Ammonium Sulfate, 17% PEG 3000, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.17α = 90
b = 54.495β = 90
c = 83.158γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.655099.90.068276.698435
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7199.90.5043.96.1

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 REPLACEMENTTHROUGHOUT5BVU1.655091591469999.180.15810.156920.18115RANDOM16.266
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]
-0.010.05-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.158
r_dihedral_angle_4_deg18.404
r_dihedral_angle_3_deg12.107
r_dihedral_angle_1_deg6.171
r_long_range_B_refined4.506
r_long_range_B_other4.226
r_scangle_other1.904
r_mcangle_it1.516
r_mcangle_other1.516
r_angle_refined_deg1.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.158
r_dihedral_angle_4_deg18.404
r_dihedral_angle_3_deg12.107
r_dihedral_angle_1_deg6.171
r_long_range_B_refined4.506
r_long_range_B_other4.226
r_scangle_other1.904
r_mcangle_it1.516
r_mcangle_other1.516
r_angle_refined_deg1.258
r_scbond_it1.154
r_scbond_other1.154
r_mcbond_it0.888
r_mcbond_other0.887
r_angle_other_deg0.77
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms6221
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing