5AGH

Crystal structure of the LeuRS editing domain of Candida albicans Mutant K510A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WFGPDB ENTRY 2WFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
140.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0, 24% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0138.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.349α = 90
b = 41.104β = 106.71
c = 67.264γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
11.816490.50.0720.84.9189762
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)
11.811.85490.52.64.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WFG1.8164.421867699890.440.167760.16510.21844RANDOM27.545
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]
-0.10.5-0.520.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.789
r_dihedral_angle_3_deg14.649
r_dihedral_angle_4_deg11.777
r_dihedral_angle_1_deg5.994
r_mcangle_it3.226
r_scbond_it2.619
r_mcbond_it1.981
r_mcbond_other1.979
r_angle_refined_deg1.441
r_angle_other_deg0.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.789
r_dihedral_angle_3_deg14.649
r_dihedral_angle_4_deg11.777
r_dihedral_angle_1_deg5.994
r_mcangle_it3.226
r_scbond_it2.619
r_mcbond_it1.981
r_mcbond_other1.979
r_angle_refined_deg1.441
r_angle_other_deg0.757
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms1932
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
DENZOdata scaling
PHASERphasing