7WPN

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5300Sodium cacodylate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0640.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.487α = 90
b = 72.053β = 90
c = 115.488γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2021-05-21MSINGLE 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
12.461.1399.90.1410.64.720367
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.80.543.1

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 REPLACEMENTTHROUGHOUT7WPM2.461.1319264105699.790.21890.21670.2593RANDOM21.865
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]
0.031.32-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.082
r_dihedral_angle_3_deg16.653
r_dihedral_angle_4_deg11.537
r_dihedral_angle_1_deg5.306
r_angle_refined_deg1.224
r_angle_other_deg0.939
r_chiral_restr0.243
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.082
r_dihedral_angle_3_deg16.653
r_dihedral_angle_4_deg11.537
r_dihedral_angle_1_deg5.306
r_angle_refined_deg1.224
r_angle_other_deg0.939
r_chiral_restr0.243
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3849
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms83

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
MOLREPphasing