☰ Navigation Tabs
Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 10mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM GDP
Crystal Properties Matthews coefficient Solvent content 3.07 59.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.335 α = 90 b = 256.08 β = 90.04 c = 88.575 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 2023-10-12 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 47.3 97.9 0.11199999999999999 0.12 0.998 16.79 7.2 181214
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 0.912 0.985 0.821
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 47.3 172153 9061 97.93 0.19985 0.19808 0.2056 0.23364 0.2419 RANDOM 30.454
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] -2.02 -0.41 0.17 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 18.024 r_long_range_B_refined 7.691 r_long_range_B_other 7.691 r_scangle_other 5.74 r_mcangle_it 4.166 r_mcangle_other 4.166 r_scbond_it 3.752 r_scbond_other 3.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 18.024 r_long_range_B_refined 7.691 r_long_range_B_other 7.691 r_scangle_other 5.74 r_mcangle_it 4.166 r_mcangle_other 4.166 r_scbond_it 3.752 r_scbond_other 3.751 r_dihedral_angle_1_deg 3.211 r_mcbond_it 2.984 r_mcbond_other 2.983 r_angle_other_deg 2.423 r_angle_refined_deg 1.832 r_chiral_restr 0.131 r_bond_other_d 0.036 r_bond_refined_d 0.019 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 15360 Nucleic Acid Atoms Solvent Atoms 1806 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing