5FOD

Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1) containing deletions of insertions 1 and 3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES (PH 7.5), 20% (W/V) PEG 10000, AND 8% ETHYLENEGLYCOL
Crystal Properties
Matthews coefficientSolvent content
237

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.6α = 88.4
b = 53.1β = 73.7
c = 62.7γ = 89.8
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.715940.0962.7620512
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)
11.71.75880.90.82

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 REPLACEMENTTHROUGHOUTPLASMODIUM KNOWLESI LEURS EDITING DOMAIN1.760.1659030302093.750.205170.202620.25506RANDOM34.07
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]
-1.110.43-0.83-0.11-0.430.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_3_deg14.519
r_dihedral_angle_4_deg12.518
r_dihedral_angle_1_deg6.252
r_mcangle_it3.703
r_scbond_it3.405
r_mcbond_it2.573
r_mcbond_other2.566
r_angle_refined_deg1.607
r_angle_other_deg0.985
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_3_deg14.519
r_dihedral_angle_4_deg12.518
r_dihedral_angle_1_deg6.252
r_mcangle_it3.703
r_scbond_it3.405
r_mcbond_it2.573
r_mcbond_other2.566
r_angle_refined_deg1.607
r_angle_other_deg0.985
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5093
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing