8OT8

Alditol oxidase from Actinomycetota bacterium in complex with D-xylulose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VFV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.12 M Monosaccharides 0.1 M Buffer System 2 7.5 30 % v/v Precipitant Mix 1
Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.442α = 90
b = 109.911β = 90
c = 296.709γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.999990SLSX06SA

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
12.449.5599.80.1680.1830.0710.9977.26.773369
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)
12.42.4599.82.5812.7981.0710.5876.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.449.5569620365499.720.248380.24630.28862RANDOM67.423
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]
10.06-2.28-7.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.438
r_dihedral_angle_4_deg17.421
r_dihedral_angle_3_deg15.887
r_long_range_B_refined10.708
r_long_range_B_other10.705
r_dihedral_angle_1_deg7.975
r_mcangle_it7.869
r_mcangle_other7.869
r_scangle_other7.446
r_mcbond_it5.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.438
r_dihedral_angle_4_deg17.421
r_dihedral_angle_3_deg15.887
r_long_range_B_refined10.708
r_long_range_B_other10.705
r_dihedral_angle_1_deg7.975
r_mcangle_it7.869
r_mcangle_other7.869
r_scangle_other7.446
r_mcbond_it5.189
r_mcbond_other5.189
r_scbond_it4.707
r_scbond_other4.705
r_angle_refined_deg1.547
r_angle_other_deg1.18
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms12414
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms252

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing