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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 8XW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 298 60 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM UDP
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.809 α = 90 b = 403.204 β = 90 c = 113.593 γ = 90
Symmetry Space Group P 21 21 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 Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror 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 1.89 48.17 99.8 0.062 0.079 0.996 6.23 13.34 423736
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 1.89 2 0.307 0.399 0.856
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.89 48.16 402543 21187 99.75 0.16721 0.16524 0.20472 0.2097 RANDOM 36.73
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] 0.93 0.55 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.689 r_dihedral_angle_4_deg 17.062 r_dihedral_angle_3_deg 14.642 r_long_range_B_refined 8.073 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 6.745 r_scangle_other 6.67 r_scbond_it 4.42 r_scbond_other 4.42 r_mcangle_it 4.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.689 r_dihedral_angle_4_deg 17.062 r_dihedral_angle_3_deg 14.642 r_long_range_B_refined 8.073 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 6.745 r_scangle_other 6.67 r_scbond_it 4.42 r_scbond_other 4.42 r_mcangle_it 4.152 r_mcangle_other 4.152 r_mcbond_it 3.131 r_mcbond_other 3.131 r_angle_other_deg 2.346 r_angle_refined_deg 1.719 r_chiral_restr 0.08 r_bond_other_d 0.036 r_gen_planes_other 0.013 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 3849 Heterogen Atoms 406
Software Software Software Name Purpose REFMAC refinement XDS data scaling MOLREP phasing XDS data reduction