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1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 11.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (B9), 1.8M Ammonium citrate pH=7.0;
Cryo: 1.8M Ammonium citrate pH=7.0, 25% Sucrose.
Crystal Properties Matthews coefficient Solvent content 3.07 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.713 α = 90 b = 120.713 β = 90 c = 70.614 γ = 120
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 C(111) 2017-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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) 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 1.3 30 99.8 0.049 0.049 0.057 0.029 22.2 3.5 285243 -3 15.5
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 1.3 1.32 100 0.599 0.599 0.712 0.378 0.725 2.3 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3SG1 1.3 27.77 268642 13851 99.77 0.14528 0.14478 0.1491 0.15494 0.1599 RANDOM 17.4
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] 0.22 0.11 0.22 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.431 r_dihedral_angle_4_deg 14.597 r_dihedral_angle_3_deg 10.512 r_long_range_B_refined 5.472 r_long_range_B_other 4.967 r_dihedral_angle_1_deg 4.474 r_scangle_other 2.761 r_scbond_it 1.785 r_scbond_other 1.779 r_angle_refined_deg 1.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.431 r_dihedral_angle_4_deg 14.597 r_dihedral_angle_3_deg 10.512 r_long_range_B_refined 5.472 r_long_range_B_other 4.967 r_dihedral_angle_1_deg 4.474 r_scangle_other 2.761 r_scbond_it 1.785 r_scbond_other 1.779 r_angle_refined_deg 1.595 r_mcangle_it 1.444 r_mcangle_other 1.444 r_mcbond_it 0.923 r_mcbond_other 0.92 r_angle_other_deg 0.413 r_chiral_restr 0.075 r_gen_planes_refined 0.057 r_gen_planes_other 0.055 r_bond_refined_d 0.007 r_bond_other_d 0.001 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 6336 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing