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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 10mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM ADP
Crystal Properties Matthews coefficient Solvent content 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.184 α = 90 b = 255.539 β = 90 c = 88.133 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror 2023-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 47.22 100 0.067 0.071 1 19.63 9.2 81724
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) Redundancy Number Unique Reflections (All) 1 2.1 2.22 0.938 0.998 0.895
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 47.21 77629 4086 99.95 0.18815 0.18615 0.1958 0.22684 0.2315 RANDOM 53.046
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 -2.09 5.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 18.2 r_dihedral_angle_3_deg 17.4 r_long_range_B_refined 9.804 r_long_range_B_other 9.803 r_scangle_other 8.111 r_dihedral_angle_1_deg 6.916 r_mcangle_it 6.22 r_mcangle_other 6.219 r_scbond_it 5.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 18.2 r_dihedral_angle_3_deg 17.4 r_long_range_B_refined 9.804 r_long_range_B_other 9.803 r_scangle_other 8.111 r_dihedral_angle_1_deg 6.916 r_mcangle_it 6.22 r_mcangle_other 6.219 r_scbond_it 5.505 r_scbond_other 5.504 r_mcbond_it 4.533 r_mcbond_other 4.52 r_angle_other_deg 2.345 r_angle_refined_deg 1.657 r_chiral_restr 0.073 r_bond_other_d 0.036 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 7672 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing