5WSB

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, allosteric activators AMP and Glucose 6-Phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WRP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227713% 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, 5 mM AMP, 5 mM D-glucose 6-phosphate
Crystal Properties
Matthews coefficientSolvent content
3.2361.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.631α = 90
b = 125.631β = 90
c = 144.514γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2016-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian SynchrotronMX1

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
12.2562.8299.39.95.1120301
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.2992.11.42.8

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 REPLACEMENTTHROUGHOUT5WRP2.2562.82114312594499.340.188980.186960.22782RANDOM36.436
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]
9.059.05-18.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.523
r_dihedral_angle_4_deg18.805
r_dihedral_angle_3_deg17.066
r_dihedral_angle_1_deg6.431
r_long_range_B_refined4.532
r_long_range_B_other4.529
r_mcangle_it2.957
r_mcangle_other2.957
r_scangle_other2.925
r_scbond_it2.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.523
r_dihedral_angle_4_deg18.805
r_dihedral_angle_3_deg17.066
r_dihedral_angle_1_deg6.431
r_long_range_B_refined4.532
r_long_range_B_other4.529
r_mcangle_it2.957
r_mcangle_other2.957
r_scangle_other2.925
r_scbond_it2.195
r_scbond_other2.16
r_mcbond_it2.117
r_mcbond_other2.117
r_angle_refined_deg1.324
r_angle_other_deg0.666
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms14172
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms195

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing