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Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 8.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 2mM PLP;
Screen: Classics II (B11), 2.1M DL-Malic acid pH 7.0;
Cryo: 25% glycerol in screen solution.
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.464 α = 90 b = 81.413 β = 94.6 c = 139.465 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 CCD MARMOSAIC 300 mm CCD Be 2021-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.43 30 94.4 0.078 0.078 0.087 0.039 0.995 19.5 4.8 167626 -3 13.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.45 90.6 0.853 0.853 0.96 0.434 0.792 1.9 4.4
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 SAD THROUGHOUT 1.43 29.29 159092 8365 94.3 0.1578 0.1568 0.1567 0.1769 0.1758 RANDOM 16.724
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] -0.33 0.02 -0.47 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.343 r_dihedral_angle_4_deg 18.413 r_dihedral_angle_3_deg 9.198 r_dihedral_angle_1_deg 4.095 r_angle_refined_deg 1.381 r_angle_other_deg 0.373 r_chiral_restr 0.069 r_gen_planes_refined 0.056 r_gen_planes_other 0.051 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.343 r_dihedral_angle_4_deg 18.413 r_dihedral_angle_3_deg 9.198 r_dihedral_angle_1_deg 4.095 r_angle_refined_deg 1.381 r_angle_other_deg 0.373 r_chiral_restr 0.069 r_gen_planes_refined 0.056 r_gen_planes_other 0.051 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7592 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing