7WQ0

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment and ATP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5300Sodium cacodylate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0941.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.276α = 90
b = 72.716β = 90
c = 118.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2021-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97914SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.0946.0299.70.1530.1670.0650.9919.46.530973
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.092.15970.5080.5570.2250.8726

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 REPLACEMENTTHROUGHOUT7WPK2.0946.0229369154499.580.21450.21260.2494RANDOM19.778
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]
2.08-0.21-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg15.428
r_dihedral_angle_3_deg14.57
r_dihedral_angle_1_deg5.957
r_angle_refined_deg1.183
r_angle_other_deg1.142
r_chiral_restr0.049
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg15.428
r_dihedral_angle_3_deg14.57
r_dihedral_angle_1_deg5.957
r_angle_refined_deg1.183
r_angle_other_deg1.142
r_chiral_restr0.049
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4182
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing