7WPT

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment M2-80 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
2.2745.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.993α = 90
b = 76.536β = 90
c = 118.642γ = 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)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
12.2664.3193.20.0712.23.424773
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)
12.262.40998.10.543

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 REPLACEMENTTHROUGHOUT7WPM2.2664.3123442127292.920.22360.22110.2673RANDOM45.547
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]
2.36-1.35-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_4_deg20.266
r_dihedral_angle_3_deg18.46
r_dihedral_angle_1_deg5.859
r_angle_refined_deg1.213
r_angle_other_deg1.158
r_chiral_restr0.055
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_4_deg20.266
r_dihedral_angle_3_deg18.46
r_dihedral_angle_1_deg5.859
r_angle_refined_deg1.213
r_angle_other_deg1.158
r_chiral_restr0.055
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3903
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms63

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
MOLREPphasing