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Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate
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 6.5 298 1% Tacsimate pH 6.0, 50mM BIS-TRIS pH 6.5, 10%PEG3350, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM Oxalate
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.051 α = 90 b = 118.353 β = 108.93 c = 99.82 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. 2022-02-05 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 48.3 99.7 0.09 0.09699999999999999 0.996 10.84 6.96 215295
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 0.8690000000000001 0.9390000000000001 0.873
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 48.3 204517 10764 99.74 0.20103 0.19865 0.2054 0.24584 0.2492 RANDOM 44.738
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 0.77 0.97 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_3_deg 17.853 r_dihedral_angle_4_deg 17.794 r_long_range_B_refined 9.565 r_long_range_B_other 9.317 r_dihedral_angle_1_deg 6.472 r_scangle_other 6.415 r_mcangle_it 4.957 r_mcangle_other 4.957 r_scbond_it 4.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_3_deg 17.853 r_dihedral_angle_4_deg 17.794 r_long_range_B_refined 9.565 r_long_range_B_other 9.317 r_dihedral_angle_1_deg 6.472 r_scangle_other 6.415 r_mcangle_it 4.957 r_mcangle_other 4.957 r_scbond_it 4.391 r_scbond_other 4.391 r_mcbond_it 3.779 r_mcbond_other 3.779 r_angle_other_deg 2.334 r_angle_refined_deg 1.556 r_chiral_restr 0.072 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 15347 Nucleic Acid Atoms Solvent Atoms 1019 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing