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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate 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 6.75 298 8%(w/v) PEG3350, 50mM Citric acid/Bis-Tris Propan(3.75:6.25) pH6.75, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 5mM PEP, 10mM FBP
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 221.061 α = 90 b = 86.644 β = 100.86 c = 258.148 γ = 90
Symmetry Space Group C 1 2 1
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. 2023-01-21 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 1.8 48.37 99.6 0.063 0.068 0.9990000000000001 14.83 6.99 442679
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 1.8 1.91 1.0290000000000001 1.11 0.8009999999999999
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 1.8 48.37 420531 22134 99.59 0.18448 0.18253 0.1913 0.22121 0.2274 RANDOM 39.959
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] -0.89 0.75 -0.55 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.982 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 15.851 r_long_range_B_refined 8.66 r_long_range_B_other 8.523 r_scangle_other 6.91 r_dihedral_angle_1_deg 6.748 r_scbond_other 4.759 r_scbond_it 4.758 r_mcangle_it 4.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.982 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 15.851 r_long_range_B_refined 8.66 r_long_range_B_other 8.523 r_scangle_other 6.91 r_dihedral_angle_1_deg 6.748 r_scbond_other 4.759 r_scbond_it 4.758 r_mcangle_it 4.401 r_mcangle_other 4.401 r_mcbond_it 3.485 r_mcbond_other 3.484 r_angle_other_deg 2.356 r_angle_refined_deg 1.762 r_chiral_restr 0.084 r_bond_other_d 0.036 r_gen_planes_other 0.014 r_bond_refined_d 0.011 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 30720 Nucleic Acid Atoms Solvent Atoms 2689 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing