5O0S

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with unreacted beta Cyclophellitol Cyclosulfate probe ME711


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293100 mM MES pH 6.5 0.2 M Ammonium Sulfate 16% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.17α = 90
b = 53.731β = 90
c = 83.138γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.1659.391000.0720.040.99911.37.9275502
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)
11.161.181002.091.140.51517.5

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 REPLACEMENTTHROUGHOUT5fjs1.1659.392615881381399.960.140090.138870.16298Same as 5NPF17.91
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]
-0.36-1.652.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.982
r_sphericity_free30.854
r_dihedral_angle_4_deg19.592
r_sphericity_bonded17.621
r_dihedral_angle_3_deg12.05
r_long_range_B_refined6.575
r_long_range_B_other6.575
r_dihedral_angle_1_deg6.543
r_rigid_bond_restr2.853
r_scangle_other2.703
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.982
r_sphericity_free30.854
r_dihedral_angle_4_deg19.592
r_sphericity_bonded17.621
r_dihedral_angle_3_deg12.05
r_long_range_B_refined6.575
r_long_range_B_other6.575
r_dihedral_angle_1_deg6.543
r_rigid_bond_restr2.853
r_scangle_other2.703
r_scbond_it2.301
r_scbond_other2.301
r_mcangle_other2.248
r_mcangle_it2.246
r_angle_refined_deg1.785
r_mcbond_it1.778
r_mcbond_other1.758
r_angle_other_deg1.031
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6225
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing