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Crystal structure of Streptococcus pneumoniae pyruvate kinase
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 5.5 298 50mM Sodium citrate pH5.5, 11% PEG1000, 10mM Na HEPES pH7.5, 75mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.9 57.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.094 α = 101.22 b = 84.705 β = 96.82 c = 107.012 γ = 91.42
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. 2021-11-26 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 49.07 96.7 0.087 0.102 0.997 9.78 3.58 168397
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 0.785 0.929 0.6920000000000001
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 49.07 159970 8420 96.77 0.17996 0.17809 0.1855 0.21519 0.2195 RANDOM 39.222
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] 0.75 -0.34 0.29 1.56 -0.93 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 18.494 r_long_range_B_refined 8.77 r_long_range_B_other 8.762 r_scangle_other 7.002 r_scbond_it 4.55 r_scbond_other 4.549 r_dihedral_angle_1_deg 4.427 r_mcangle_it 4.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 18.494 r_long_range_B_refined 8.77 r_long_range_B_other 8.762 r_scangle_other 7.002 r_scbond_it 4.55 r_scbond_other 4.549 r_dihedral_angle_1_deg 4.427 r_mcangle_it 4.286 r_mcangle_other 4.286 r_mcbond_it 3.18 r_mcbond_other 3.175 r_angle_other_deg 2.304 r_angle_refined_deg 1.465 r_chiral_restr 0.073 r_bond_other_d 0.036 r_bond_refined_d 0.011 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 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 15344 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing