8IAT

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52981% Tacsimate pH 6.0, 50mM BIS-TRIS pH 6.5, 10%PEG3350, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM Oxalate
Crystal Properties
Matthews coefficientSolvent content
2.652.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 212.051α = 90
b = 118.353β = 108.93
c = 99.82γ = 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.2022-02-05MSINGLE 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
11.848.399.70.090.096999999999999990.99610.846.96215295
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)
11.81.910.86900000000000010.93900000000000010.873

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 REPLACEMENTTHROUGHOUT1.848.32045171076499.740.201030.198650.24584RANDOM44.738
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]
-20.770.970.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.867
r_dihedral_angle_3_deg17.853
r_dihedral_angle_4_deg17.794
r_long_range_B_refined9.565
r_long_range_B_other9.317
r_dihedral_angle_1_deg6.472
r_scangle_other6.415
r_mcangle_it4.957
r_mcangle_other4.957
r_scbond_it4.391
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.867
r_dihedral_angle_3_deg17.853
r_dihedral_angle_4_deg17.794
r_long_range_B_refined9.565
r_long_range_B_other9.317
r_dihedral_angle_1_deg6.472
r_scangle_other6.415
r_mcangle_it4.957
r_mcangle_other4.957
r_scbond_it4.391
r_scbond_other4.391
r_mcbond_it3.779
r_mcbond_other3.779
r_angle_other_deg2.334
r_angle_refined_deg1.556
r_chiral_restr0.072
r_bond_other_d0.036
r_gen_planes_other0.01
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms15347
Nucleic Acid Atoms
Solvent Atoms1019
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing