6HCV

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with a chromone ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52910.1 M Bis-Tris pH 6.5, 2 % Tascimate pH 6.0, 20 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5150.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.557α = 90
b = 95.189β = 90
c = 166.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442016-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.24898.70.1194.859459
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)
12.22.2690.30.3840.492.32.4

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 REPLACEMENTTHROUGHOUT4H022.24856406299898.610.21510.2130.2542RANDOM28.78
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]
0.15-0.160.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.527
r_dihedral_angle_3_deg15.997
r_dihedral_angle_4_deg15.109
r_dihedral_angle_1_deg6.536
r_angle_other_deg1.72
r_angle_refined_deg1.298
r_chiral_restr0.064
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.527
r_dihedral_angle_3_deg15.997
r_dihedral_angle_4_deg15.109
r_dihedral_angle_1_deg6.536
r_angle_other_deg1.72
r_angle_refined_deg1.298
r_chiral_restr0.064
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7792
Nucleic Acid Atoms
Solvent Atoms539
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing