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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 16.5% PEG300,50mM Na Acetate pH4.2, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM FBP, 10mM Oxalate
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.442 α = 88.95 b = 114.66 β = 88.12 c = 140.705 γ = 76.52
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. 2022-04-21 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 49.38 97 0.08 0.094 0.997 8.85 3.6 293893
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 2.12 0.9179999999999999 1.075 0.598
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 49.38 279192 14695 96.95 0.20201 0.19966 0.206 0.24609 0.249 RANDOM 46.44
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] 1.54 2.05 0.05 0.35 -0.02 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 19.688 r_dihedral_angle_3_deg 17.862 r_long_range_B_refined 10.202 r_long_range_B_other 10.202 r_scangle_other 8.233 r_dihedral_angle_1_deg 7.01 r_mcangle_it 6.075 r_mcangle_other 6.075 r_scbond_it 5.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 19.688 r_dihedral_angle_3_deg 17.862 r_long_range_B_refined 10.202 r_long_range_B_other 10.202 r_scangle_other 8.233 r_dihedral_angle_1_deg 7.01 r_mcangle_it 6.075 r_mcangle_other 6.075 r_scbond_it 5.711 r_scbond_other 5.711 r_mcbond_it 4.608 r_mcbond_other 4.604 r_angle_other_deg 2.371 r_angle_refined_deg 1.769 r_chiral_restr 0.079 r_bond_other_d 0.036 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 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 29996 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 283
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing