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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP
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 7 298 10mM HEPES pH7.5, 75mM NaCl, 125mM KCl, 10mM Tris-HCl pH7.0, 14% PEG4000, 10mM Oxalate, 10mM FBP, 5mM UDP
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.464 α = 90 b = 81.464 β = 90 c = 398.91 γ = 90
Symmetry Space Group P 43 2 2
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 2023-12-04 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 1.75 40.74 99.5 0.057 0.063 0.9990000000000001 16.01 6 136776
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 1.75 1.85 0.9359999999999999 1.024 0.672
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 1.75 40.73 129937 6839 99.48 0.16174 0.16023 0.1712 0.19057 0.1992 RANDOM 34.335
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] 0.43 0.43 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.178 r_dihedral_angle_4_deg 16.123 r_dihedral_angle_3_deg 14.53 r_long_range_B_refined 8.55 r_long_range_B_other 8.55 r_scangle_other 7.561 r_dihedral_angle_1_deg 6.286 r_scbond_other 4.987 r_scbond_it 4.986 r_mcangle_other 3.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.178 r_dihedral_angle_4_deg 16.123 r_dihedral_angle_3_deg 14.53 r_long_range_B_refined 8.55 r_long_range_B_other 8.55 r_scangle_other 7.561 r_dihedral_angle_1_deg 6.286 r_scbond_other 4.987 r_scbond_it 4.986 r_mcangle_other 3.835 r_mcangle_it 3.832 r_mcbond_it 2.95 r_mcbond_other 2.942 r_angle_other_deg 2.351 r_angle_refined_deg 1.783 r_chiral_restr 0.091 r_bond_other_d 0.036 r_gen_planes_other 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 Atoms Number Protein Atoms 7680 Nucleic Acid Atoms Solvent Atoms 911 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing