8ZLY

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8XW9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.329860 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM UDP
Crystal Properties
Matthews coefficientSolvent content
2.9157.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.809α = 90
b = 403.204β = 90
c = 113.593γ = 90
Symmetry
Space GroupP 21 21 2

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 mirror2023-12-04MSINGLE 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
11.8948.1799.80.0620.0790.9966.2313.34423736
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)
11.8920.3070.3990.856

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 REPLACEMENTTHROUGHOUT1.8948.164025432118799.750.167210.165240.20472RANDOM36.73
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]
0.930.55-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.689
r_dihedral_angle_4_deg17.062
r_dihedral_angle_3_deg14.642
r_long_range_B_refined8.073
r_long_range_B_other8.017
r_dihedral_angle_1_deg6.745
r_scangle_other6.67
r_scbond_it4.42
r_scbond_other4.42
r_mcangle_it4.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.689
r_dihedral_angle_4_deg17.062
r_dihedral_angle_3_deg14.642
r_long_range_B_refined8.073
r_long_range_B_other8.017
r_dihedral_angle_1_deg6.745
r_scangle_other6.67
r_scbond_it4.42
r_scbond_other4.42
r_mcangle_it4.152
r_mcangle_other4.152
r_mcbond_it3.131
r_mcbond_other3.131
r_angle_other_deg2.346
r_angle_refined_deg1.719
r_chiral_restr0.08
r_bond_other_d0.036
r_gen_planes_other0.013
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 Atoms3849
Heterogen Atoms406

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
MOLREPphasing
XDSdata reduction