5NPF

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2 M Ammonium Sulfate, 23% PEG 3000, 0.1 M MES pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.18α = 90
b = 53.81β = 90
c = 83.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
11.3853.8199.30.0690.030.99915.16.1163829
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)
11.381.4293.50.9680.590.5081.33.1

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 REPLACEMENTTHROUGHOUT5bvu1.3851.57155502824599.220.127240.125450.1605RANDOM19.218
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]
1.59-1.53-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.548
r_sphericity_free33.105
r_dihedral_angle_4_deg22.629
r_sphericity_bonded16.98
r_dihedral_angle_3_deg12.168
r_dihedral_angle_1_deg6.588
r_long_range_B_other3.942
r_long_range_B_refined3.94
r_scangle_other3.393
r_scbond_it2.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.548
r_sphericity_free33.105
r_dihedral_angle_4_deg22.629
r_sphericity_bonded16.98
r_dihedral_angle_3_deg12.168
r_dihedral_angle_1_deg6.588
r_long_range_B_other3.942
r_long_range_B_refined3.94
r_scangle_other3.393
r_scbond_it2.91
r_scbond_other2.901
r_mcangle_other2.885
r_mcangle_it2.884
r_rigid_bond_restr2.468
r_mcbond_it2.358
r_mcbond_other2.352
r_angle_refined_deg1.74
r_angle_other_deg1.022
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.01
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 Atoms6185
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing