8GYY

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6KJ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.1613% PEG3350, 0.1 M Tris-HCl pH8.5, 0.2% MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.4364.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 228.429α = 90
b = 89.23β = 90
c = 218.087γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.068158.2495.10.1120.1320.06730.83.5257788
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)
12.0682.110.9130.5550.5843.3

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 REPLACEMENTTHROUGHOUT6KJ02.0735.972450681272094.960.221090.219130.25895RANDOM39.556
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]
-2.985.48-2.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.35
r_dihedral_angle_2_deg9.968
r_dihedral_angle_1_deg7.47
r_long_range_B_refined7.461
r_long_range_B_other7.449
r_scangle_other5.488
r_mcangle_it5.002
r_mcangle_other5.002
r_scbond_it3.563
r_scbond_other3.563
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.35
r_dihedral_angle_2_deg9.968
r_dihedral_angle_1_deg7.47
r_long_range_B_refined7.461
r_long_range_B_other7.449
r_scangle_other5.488
r_mcangle_it5.002
r_mcangle_other5.002
r_scbond_it3.563
r_scbond_other3.563
r_mcbond_it3.317
r_mcbond_other3.316
r_angle_refined_deg1.532
r_angle_other_deg0.517
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms24034
Nucleic Acid Atoms
Solvent Atoms1294
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing