6H0P

The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NADH and UDP-D-glucuronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H0N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.52980.8 M sodium phosphate, 0.8 M potassium phosphate, and 0.1 M sodium-HEPES (pH 7.5)
Crystal Properties
Matthews coefficientSolvent content
4.5172.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.564α = 90
b = 144.564β = 90
c = 130.519γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000040SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.4748.4499.80.1510.99813.18.320833
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.473.899.20.80.8441.97.9

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 REPLACEMENTTHROUGHOUT6H0N3.4748.4419736107399.830.198060.195890.23904RANDOM124.459
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]
3.361.683.36-10.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.346
r_dihedral_angle_4_deg23.66
r_dihedral_angle_3_deg18.101
r_long_range_B_refined14.052
r_long_range_B_other14.028
r_scangle_other11.266
r_mcangle_it10.597
r_mcangle_other10.596
r_dihedral_angle_1_deg8.131
r_scbond_it7.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.346
r_dihedral_angle_4_deg23.66
r_dihedral_angle_3_deg18.101
r_long_range_B_refined14.052
r_long_range_B_other14.028
r_scangle_other11.266
r_mcangle_it10.597
r_mcangle_other10.596
r_dihedral_angle_1_deg8.131
r_scbond_it7.501
r_scbond_other7.5
r_mcbond_it7.024
r_mcbond_other7.023
r_angle_refined_deg2.23
r_angle_other_deg1.372
r_chiral_restr0.113
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.005
r_bond_other_d0.003
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 Atoms5725
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing