8IAV

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with 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 DROP7.52989%PEG3350,150mM NH4Cl, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM FBP
Crystal Properties
Matthews coefficientSolvent content
2.6152.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 217.032α = 90
b = 86.789β = 103.22
c = 129.857γ = 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.2022-04-21MSINGLE 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
12.5947.6999.20.050.0559999999999999940.999000000000000118.215.1972422
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)
12.592.750.95400000000000011.060.89

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 REPLACEMENTTHROUGHOUT2.5947.6968784362199.220.237040.233880.29776RANDOM99.559
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]
4.015.57-7.931.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.443
r_dihedral_angle_4_deg21.027
r_dihedral_angle_3_deg19.731
r_long_range_B_refined14.32
r_long_range_B_other14.32
r_scangle_other9.656
r_mcangle_it9.319
r_mcangle_other9.319
r_dihedral_angle_1_deg7.04
r_scbond_other6.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.443
r_dihedral_angle_4_deg21.027
r_dihedral_angle_3_deg19.731
r_long_range_B_refined14.32
r_long_range_B_other14.32
r_scangle_other9.656
r_mcangle_it9.319
r_mcangle_other9.319
r_dihedral_angle_1_deg7.04
r_scbond_other6.416
r_scbond_it6.414
r_mcbond_it6.403
r_mcbond_other6.402
r_angle_other_deg2.277
r_angle_refined_deg1.493
r_chiral_restr0.071
r_bond_other_d0.035
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.006
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 Atoms13864
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing