2WFG

Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.341.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.02α = 90
b = 58.04β = 90
c = 97.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.23099.70.168.163.4912930
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2699.50.552.263.31

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 REPLACEMENTTHROUGHOUT2.249.881230062999.750.188110.18450.26155RANDOM22.96
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]
0.07-0.870.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.932
r_dihedral_angle_3_deg15.389
r_dihedral_angle_4_deg6.994
r_dihedral_angle_1_deg5.835
r_scangle_it1.854
r_angle_refined_deg1.153
r_scbond_it1.107
r_mcangle_it0.782
r_mcbond_it0.419
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.932
r_dihedral_angle_3_deg15.389
r_dihedral_angle_4_deg6.994
r_dihedral_angle_1_deg5.835
r_scangle_it1.854
r_angle_refined_deg1.153
r_scbond_it1.107
r_mcangle_it0.782
r_mcbond_it0.419
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1974
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing