7YO7

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 5 seconds


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289.1515% PEG3350, 0.1 M Tris-HCl pH8.0, 0.2% MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.6653.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.35α = 90
b = 182.57β = 90
c = 242.16γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97915SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8173.5499.90.1360.1480.0560.99710.713.3161417
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.861001.2291.3250.4950.7941.914

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 REPLACEMENTTHROUGHOUT6KJ01.8173.54160806785099.90.21370.21180.2503RANDOM35.027
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]
1.89-1.12-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg20.035
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg7.094
r_angle_refined_deg2.145
r_angle_other_deg1.165
r_chiral_restr0.138
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg20.035
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg7.094
r_angle_refined_deg2.145
r_angle_other_deg1.165
r_chiral_restr0.138
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11419
Nucleic Acid Atoms
Solvent Atoms973
Heterogen Atoms467

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing