7ULZ

Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H99pdb entry 3h99 as per Morda

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5287Anatrace MCSG1 screen, condition D8: 1.5M Ammonium sulfate + BisTris/HCl pH 6.5: PsaeA.10201.a.B1.PW38931 at 23mg/ml + 3mM L-Methionine + 3mM AMP. Tray 320141 d7: cryo: 20% EG + compounds: puck egi5-5
Crystal Properties
Matthews coefficientSolvent content
4.7574.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.9α = 90
b = 167.9β = 90
c = 72.24γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2022-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.85099.90.1180.1290.99613.116.2612909444.871
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.871000.620.6770.9332.886.323

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEpdb entry 3h99 as per Morda2.848.471.3529016188099.720.17660.1750.1999051.79
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.6496
f_angle_d0.6526
f_chiral_restr0.0425
f_plane_restr0.006
f_bond_d0.0043
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4073
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms44

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building