7QI8

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7QH8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Reservoir: 0.25 M NaOAc, 14% PEG 3350 Protein: 100 mM HEPES, 150 mM NaCl, 5% glycerol, pH 7.5, ~ 20 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.196α = 90
b = 84.196β = 90
c = 147.984γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98011SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.249.331000.2050.0920.9955.811.12780738.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.271001.7220.8110.8571.110.5

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 REPLACEMENTTHROUGHOUT7QH82.246.4326375139399.970.24670.24380.3047RANDOM59.483
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]
3.033.03-6.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.08
r_dihedral_angle_3_deg18.196
r_dihedral_angle_4_deg15.901
r_dihedral_angle_1_deg8.322
r_angle_refined_deg1.481
r_angle_other_deg1.216
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.08
r_dihedral_angle_3_deg18.196
r_dihedral_angle_4_deg15.901
r_dihedral_angle_1_deg8.322
r_angle_refined_deg1.481
r_angle_other_deg1.216
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3591
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing