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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate
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, SITTING DROP 7.5 298 Details about the temperature: 20mM MgCl2, 1mM CoCl2, 35mM Na HEPES-HCl pH7.5, 1M (NH4)2SO4, 0.5mM Spermine, 37.5mM NaCl,500mM KCl, 5mM PEP
Crystal Properties Matthews coefficient Solvent content 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.057 α = 90 b = 110.372 β = 90 c = 130.931 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. 2022-11-12 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 2.89 50 99.8 0.171 0.18899999999999997 0.995 9.68 5.56 31733
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 2.89 3.07 1.01 1.119 0.8440000000000001
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 2.89 48.58 30120 1586 99.72 0.24244 0.24082 0.2385 0.27276 0.2682 RANDOM 49.756
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] 2.19 4.37 -6.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_3_deg 21.511 r_dihedral_angle_4_deg 19.126 r_long_range_B_refined 10.614 r_long_range_B_other 10.613 r_scangle_other 6.294 r_dihedral_angle_1_deg 6.181 r_mcangle_it 5.45 r_mcangle_other 5.45 r_scbond_it 3.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_3_deg 21.511 r_dihedral_angle_4_deg 19.126 r_long_range_B_refined 10.614 r_long_range_B_other 10.613 r_scangle_other 6.294 r_dihedral_angle_1_deg 6.181 r_mcangle_it 5.45 r_mcangle_other 5.45 r_scbond_it 3.811 r_scbond_other 3.799 r_mcbond_it 3.425 r_mcbond_other 3.424 r_angle_other_deg 2.342 r_angle_refined_deg 1.477 r_chiral_restr 0.059 r_bond_other_d 0.036 r_bond_refined_d 0.007 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 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 21 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing