8IAX

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate and fructose 1,6-bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.752988%(w/v) PEG3350, 50mM Citric acid/Bis-Tris Propan(3.75:6.25) pH6.75, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 5mM PEP, 10mM FBP
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 221.061α = 90
b = 86.644β = 100.86
c = 258.148γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MMain beamline optics is a double-crystal monochromator and a horizontal focusing mirror.2023-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.848.3799.60.0630.0680.999000000000000114.836.99442679
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.911.02900000000000011.110.8009999999999999

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.848.374205312213499.590.184480.182530.22121RANDOM39.959
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]
-0.890.75-0.551.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.982
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg15.851
r_long_range_B_refined8.66
r_long_range_B_other8.523
r_scangle_other6.91
r_dihedral_angle_1_deg6.748
r_scbond_other4.759
r_scbond_it4.758
r_mcangle_it4.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.982
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg15.851
r_long_range_B_refined8.66
r_long_range_B_other8.523
r_scangle_other6.91
r_dihedral_angle_1_deg6.748
r_scbond_other4.759
r_scbond_it4.758
r_mcangle_it4.401
r_mcangle_other4.401
r_mcbond_it3.485
r_mcbond_other3.484
r_angle_other_deg2.356
r_angle_refined_deg1.762
r_chiral_restr0.084
r_bond_other_d0.036
r_gen_planes_other0.014
r_bond_refined_d0.011
r_gen_planes_refined0.009
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 Atoms30720
Nucleic Acid Atoms
Solvent Atoms2689
Heterogen Atoms256

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing