6WQ6

Xanthomonas citri Methionyl-tRNA synthetase in complex with methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PFY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M Tris-HCl, 28 - 32 % PEG 4000, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
1.9838

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.146α = 90
b = 83.624β = 90
c = 95.251γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

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
11.747.631000.0760.0790.022119.212.768460
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)
11.71.731001.9051.9880.5590.70912.4

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 REPLACEMENTTHROUGHOUT1PFY1.747.6364912344899.940.19550.19370.2305RANDOM34.267
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]
4.03-3.1-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.361
r_dihedral_angle_3_deg16.656
r_dihedral_angle_4_deg14.357
r_dihedral_angle_1_deg6.041
r_angle_refined_deg1.862
r_angle_other_deg1.064
r_chiral_restr0.112
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.361
r_dihedral_angle_3_deg16.656
r_dihedral_angle_4_deg14.357
r_dihedral_angle_1_deg6.041
r_angle_refined_deg1.862
r_angle_other_deg1.064
r_chiral_restr0.112
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4245
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction