6HCU

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H02 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1 M Bis-Tris pH 6.5, 2 % (v/v) Tascimate pH 6.0, 20 % (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.137α = 90
b = 95.344β = 90
c = 166.517γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.074ESRFID29

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
11.628399.90.062104.3148069
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)
11.621.661000.8720.591.74.4

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 REPLACEMENTTHROUGHOUT4H021.6282.74139948728099.260.18480.18270.226RANDOM25.892
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]
0.350.53-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.035
r_dihedral_angle_4_deg16.996
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg7.168
r_angle_refined_deg2.245
r_angle_other_deg1.181
r_chiral_restr0.152
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.035
r_dihedral_angle_4_deg16.996
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg7.168
r_angle_refined_deg2.245
r_angle_other_deg1.181
r_chiral_restr0.152
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7860
Nucleic Acid Atoms
Solvent Atoms966
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
MOLREPphasing