8IAW

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Details about the temperature: 20mM MgCl2, 1mM CoCl2, 35mM Na HEPES-HCl pH7.5, 1M (NH4)2SO4, 0.5mM Spermine, 37.5mM NaCl,500mM KCl, 5mM PEP
Crystal Properties
Matthews coefficientSolvent content
3.0459.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.057α = 90
b = 110.372β = 90
c = 130.931γ = 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 mirror.2022-11-12MSINGLE 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
12.895099.80.1710.188999999999999970.9959.685.5631733
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)
12.893.071.011.1190.8440000000000001

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 REPLACEMENTTHROUGHOUT2.8948.5830120158699.720.242440.240820.27276RANDOM49.756
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]
2.194.37-6.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.997
r_dihedral_angle_3_deg21.511
r_dihedral_angle_4_deg19.126
r_long_range_B_refined10.614
r_long_range_B_other10.613
r_scangle_other6.294
r_dihedral_angle_1_deg6.181
r_mcangle_it5.45
r_mcangle_other5.45
r_scbond_it3.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.997
r_dihedral_angle_3_deg21.511
r_dihedral_angle_4_deg19.126
r_long_range_B_refined10.614
r_long_range_B_other10.613
r_scangle_other6.294
r_dihedral_angle_1_deg6.181
r_mcangle_it5.45
r_mcangle_other5.45
r_scbond_it3.811
r_scbond_other3.799
r_mcbond_it3.425
r_mcbond_other3.424
r_angle_other_deg2.342
r_angle_refined_deg1.477
r_chiral_restr0.059
r_bond_other_d0.036
r_bond_refined_d0.007
r_gen_planes_other0.006
r_gen_planes_refined0.005
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 Atoms7680
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing