8XW9 | pdb_00008xw9

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729810mM HEPES pH7.5, 75mM NaCl, 125mM KCl, 10mM Tris-HCl pH7.0, 14% PEG4000, 10mM Oxalate, 10mM FBP, 5mM UDP
Crystal Properties
Matthews coefficientSolvent content
2.957.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.464α = 90
b = 81.464β = 90
c = 398.91γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-12-04MSINGLE 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
11.7540.7499.50.0570.0630.999000000000000116.016136776
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)
11.751.850.93599999999999991.0240.672

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 REPLACEMENTTHROUGHOUT1.7540.73129937683999.480.161740.160230.170.190570.2RANDOM34.335
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]
0.430.43-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.178
r_dihedral_angle_4_deg16.123
r_dihedral_angle_3_deg14.53
r_long_range_B_refined8.55
r_long_range_B_other8.55
r_scangle_other7.561
r_dihedral_angle_1_deg6.286
r_scbond_other4.987
r_scbond_it4.986
r_mcangle_other3.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.178
r_dihedral_angle_4_deg16.123
r_dihedral_angle_3_deg14.53
r_long_range_B_refined8.55
r_long_range_B_other8.55
r_scangle_other7.561
r_dihedral_angle_1_deg6.286
r_scbond_other4.987
r_scbond_it4.986
r_mcangle_other3.835
r_mcangle_it3.832
r_mcbond_it2.95
r_mcbond_other2.942
r_angle_other_deg2.351
r_angle_refined_deg1.783
r_chiral_restr0.091
r_bond_other_d0.036
r_gen_planes_other0.017
r_bond_refined_d0.014
r_gen_planes_refined0.011
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 Atoms911
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing