5WS8

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227712% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP
Crystal Properties
Matthews coefficientSolvent content
3.3263.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.011α = 90
b = 127.011β = 90
c = 144.652γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6263.5110010.65.578513
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.622.671002.25.5

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 REPLACEMENTTHROUGHOUT5WRP2.6263.5174461401199.950.175620.17340.21784RANDOM68.639
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]
1.810.91.81-5.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.177
r_dihedral_angle_4_deg22.034
r_dihedral_angle_3_deg19.867
r_long_range_B_refined9.497
r_long_range_B_other9.479
r_scangle_other5.664
r_dihedral_angle_1_deg5.446
r_mcangle_it4.826
r_mcangle_other4.826
r_scbond_it3.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.177
r_dihedral_angle_4_deg22.034
r_dihedral_angle_3_deg19.867
r_long_range_B_refined9.497
r_long_range_B_other9.479
r_scangle_other5.664
r_dihedral_angle_1_deg5.446
r_mcangle_it4.826
r_mcangle_other4.826
r_scbond_it3.67
r_scbond_other3.651
r_mcbond_it3.094
r_mcbond_other3.091
r_angle_refined_deg1.181
r_angle_other_deg0.651
r_chiral_restr0.072
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14008
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing