8IAS

Crystal structure of Streptococcus pneumoniae pyruvate kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529850mM Sodium citrate pH5.5, 11% PEG1000, 10mM Na HEPES pH7.5, 75mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.957.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.094α = 101.22
b = 84.705β = 96.82
c = 107.012γ = 91.42
Symmetry
Space GroupP 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.2021-11-26MSINGLE 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
1249.0796.70.0870.1020.9979.783.58168397
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)
122.120.7850.9290.6920000000000001

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 REPLACEMENTTHROUGHOUT249.07159970842096.770.179960.178090.21519RANDOM39.222
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]
0.75-0.340.291.56-0.93-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg18.494
r_long_range_B_refined8.77
r_long_range_B_other8.762
r_scangle_other7.002
r_scbond_it4.55
r_scbond_other4.549
r_dihedral_angle_1_deg4.427
r_mcangle_it4.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.681
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg18.494
r_long_range_B_refined8.77
r_long_range_B_other8.762
r_scangle_other7.002
r_scbond_it4.55
r_scbond_other4.549
r_dihedral_angle_1_deg4.427
r_mcangle_it4.286
r_mcangle_other4.286
r_mcbond_it3.18
r_mcbond_other3.175
r_angle_other_deg2.304
r_angle_refined_deg1.465
r_chiral_restr0.073
r_bond_other_d0.036
r_bond_refined_d0.011
r_gen_planes_other0.008
r_gen_planes_refined0.006
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 Atoms15344
Nucleic Acid Atoms
Solvent Atoms857
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing