8XW7 | pdb_00008xw7

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8XW6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829810mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM ADP
Crystal Properties
Matthews coefficientSolvent content
3.0459.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.184α = 90
b = 255.539β = 90
c = 88.133γ = 90
Symmetry
Space GroupC 2 2 21

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 mirror2023-10-12MSINGLE 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
12.147.221000.0670.071119.639.281724
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)
12.12.220.9380.9980.895

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.147.2177629408699.950.188150.186150.20.226840.23RANDOM53.046
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]
-3.85-2.095.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.479
r_dihedral_angle_4_deg18.2
r_dihedral_angle_3_deg17.4
r_long_range_B_refined9.804
r_long_range_B_other9.803
r_scangle_other8.111
r_dihedral_angle_1_deg6.916
r_mcangle_it6.22
r_mcangle_other6.219
r_scbond_it5.505
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.479
r_dihedral_angle_4_deg18.2
r_dihedral_angle_3_deg17.4
r_long_range_B_refined9.804
r_long_range_B_other9.803
r_scangle_other8.111
r_dihedral_angle_1_deg6.916
r_mcangle_it6.22
r_mcangle_other6.219
r_scbond_it5.505
r_scbond_other5.504
r_mcbond_it4.533
r_mcbond_other4.52
r_angle_other_deg2.345
r_angle_refined_deg1.657
r_chiral_restr0.073
r_bond_other_d0.036
r_bond_refined_d0.01
r_gen_planes_other0.01
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 Atoms7672
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing